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- PDB-8to0: 48-nm repeating structure of doublets from mouse sperm flagella -

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Basic information

Entry
Database: PDB / ID: 8to0
Title48-nm repeating structure of doublets from mouse sperm flagella
Components
  • (Cilia- and flagella-associated protein ...) x 9
  • (EF-hand domain-containing family member ...) x 2
  • (Piercer of microtubule wall ...) x 2
  • Cilia- and flagella- associated protein 210
  • Coiled-coil domain-containing protein 105
  • Detyrosinated tubulin alpha-1A chain
  • Dual specificity protein phosphatase 3
  • EF-hand calcium-binding domain-containing protein 6
  • EF-hand domain-containing protein 1
  • Enkurin
  • Meiosis-specific nuclear structural protein 1
  • Nucleoside diphosphate kinase 7Nucleoside-diphosphate kinase
  • Parkin coregulated gene protein homolog
  • Protein FAM166B
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm acrosome-associated protein 9
  • Sperm-associated antigen 8
  • Tektin bundle-interacting protein 1
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tektin-5
  • Tubulin beta-4B chain
KeywordsSTRUCTURAL PROTEIN / Mammalian sperm / axoneme / microtubule-based structure / microtubule inner protein / non-motor proteins / cellular motility / fertility
Function / homology
Function and homology information


ERKs are inactivated / protein localization to motile cilium / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly ...ERKs are inactivated / protein localization to motile cilium / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / regulation of calcineurin-NFAT signaling cascade / MAP kinase phosphatase activity / Intraflagellar transport / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / positive regulation of feeding behavior / cerebrospinal fluid circulation / sperm principal piece / COPI-independent Golgi-to-ER retrograde traffic / regulation of cilium beat frequency involved in ciliary motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cilium movement involved in extracellular fluid movement / cilium movement involved in cell motility / intraciliary transport / negative regulation of chemotaxis / 9+2 motile cilium / regulation of store-operated calcium entry / PKR-mediated signaling / COPI-mediated anterograde transport / cilium movement / Aggrephagy / Transferases; Transferring phosphorus-containing groups / calcium ion sensor activity / acrosomal membrane / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / axoneme assembly / The role of GTSE1 in G2/M progression after G2 checkpoint / flagellated sperm motility / cilium organization / Recycling pathway of L1 / negative regulation of T cell activation / axonemal microtubule / left/right axis specification / COPI-dependent Golgi-to-ER retrograde traffic / gamma-tubulin ring complex / RHO GTPases Activate Formins / Separation of Sister Chromatids / Hedgehog 'off' state / organelle transport along microtubule / glial cell differentiation / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / protein tyrosine/serine/threonine phosphatase activity / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / forebrain morphogenesis / neuron projection arborization / Regulation of PLK1 Activity at G2/M Transition / manchette / positive regulation of focal adhesion disassembly / positive regulation of cilium assembly / cerebellar cortex morphogenesis / dentate gyrus development / MHC class II antigen presentation / pyramidal neuron differentiation / negative regulation of JNK cascade / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / GTP biosynthetic process / centrosome cycle / intermediate filament / motor behavior / microtubule organizing center / nucleoside diphosphate kinase activity / tubulin complex / response to L-glutamate / ciliary base / negative regulation of T cell receptor signaling pathway / regulation of focal adhesion assembly / smoothened signaling pathway / myosin phosphatase activity / adult behavior / intercellular bridge / regulation of synapse organization / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of MAPK cascade / negative regulation of epidermal growth factor receptor signaling pathway
Similarity search - Function
DJBP, EF-hand domain / Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / EF-hand domain / Tektin bundle interacting protein 1 / Atypical dual specificity phosphatase, subfamily A / Sperm-associated antigen 8 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain ...DJBP, EF-hand domain / Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / EF-hand domain / Tektin bundle interacting protein 1 / Atypical dual specificity phosphatase, subfamily A / Sperm-associated antigen 8 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 / : / Sperm acrosome-associated protein 9 / Protein CFAP95 / Tektin / Cilia- and flagella-associated protein 276 / Tektin family / Protein of unknown function (DUF3695) / Uncharacterised protein FAM166/UPF0605 / Protein Flattop / Protein of unknown function (DUF2475) / Nucleoside diphosphate kinase 7 / Meiosis-specific nuclear structural protein 1 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 45 / NDPK7, second NDPk domain / Cilia- and flagella- associated protein 210 / CFAP53/TCHP / Trichohyalin-plectin-homology domain / Trichohyalin-plectin-homology domain / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / RIB43A / RIB43A / DM10 domain / EF-hand domain-containing protein EFHC1/EFHC2/EFHB / DM10 domain / DM10 domain profile. / Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. / Enkurin domain / Calmodulin-binding / Enkurin domain profile. / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Parkin co-regulated protein / Parkin co-regulated protein / Dual specificity phosphatase, catalytic domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / EF hand / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / EF-hand domain pair / Mir domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Tubulin/FtsZ, GTPase domain superfamily / Protein-tyrosine phosphatase-like / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cilia- and flagella- associated protein 210 / Ciliary microtubule inner protein 2B / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-1A chain / Tubulin beta-4B chain / Tektin-4 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 107 / Piercer of microtubule wall 1 protein ...Cilia- and flagella- associated protein 210 / Ciliary microtubule inner protein 2B / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-1A chain / Tubulin beta-4B chain / Tektin-4 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 107 / Piercer of microtubule wall 1 protein / Cilia- and flagella-associated protein 52 / Meiosis-specific nuclear structural protein 1 / EF-hand calcium-binding domain-containing protein 6 / Protein Flattop / Cilia- and flagella-associated protein 161 / Enkurin / Tektin-3 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 20 / EF-hand domain-containing family member B / Tektin-2 / Cilia- and flagella-associated protein 95 / Cilia- and flagella-associated protein 53 / EF-hand domain-containing family member C2 / Tektin-like protein 1 / RIB43A-like with coiled-coils protein 2 / Dual specificity protein phosphatase 3 / Cilia- and flagella-associated protein 141 / EF-hand domain-containing protein 1 / Cilia- and flagella-associated protein 45 / Cilia- and flagella-associated protein 276 / Tektin-1 / Parkin coregulated gene protein homolog / Nucleoside diphosphate kinase homolog 7 / Piercer of microtubule wall 2 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.7 Å
AuthorsChen, Z. / Shiozak, M. / Hass, K.M. / Skinner, W. / Zhao, S. / Guo, C. / Polacco, B.J. / Yu, Z. / Krogan, N.J. / Kaake, R.M. ...Chen, Z. / Shiozak, M. / Hass, K.M. / Skinner, W. / Zhao, S. / Guo, C. / Polacco, B.J. / Yu, Z. / Krogan, N.J. / Kaake, R.M. / Vale, R.D. / Agard, D.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118106 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118099 United States
CitationJournal: Cell / Year: 2023
Title: De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking.
Authors: Zhen Chen / Momoko Shiozaki / Kelsey M Haas / Will M Skinner / Shumei Zhao / Caiying Guo / Benjamin J Polacco / Zhiheng Yu / Nevan J Krogan / Polina V Lishko / Robyn M Kaake / Ronald D Vale / David A Agard /
Abstract: To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their ...To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their structures in vitro. Here, we combined cellular cryoelectron tomography (cryo-ET) and AlphaFold2 modeling to address these questions and understand how mammalian sperm are built in situ. Our cellular cryo-ET and subtomogram averaging provided 6.0-Å reconstructions of axonemal microtubule structures. The well-resolved tertiary structures allowed us to unbiasedly match sperm-specific densities with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105, and SPACA9 as novel microtubule-associated proteins. These proteins form an extensive interaction network crosslinking the lumen of axonemal doublet microtubules, suggesting their roles in modulating the mechanical properties of the filaments. Indeed, Tekt5 -/- sperm possess more deformed flagella with 180° bends. Together, our studies presented a cellular visual proteomics workflow and shed light on the in vivo functions of Tektin 5.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Cilia- and flagella-associated protein 95
L: Tektin-1
M: Tektin-1
N: Detyrosinated tubulin alpha-1A chain
O: Tubulin beta-4B chain
P: Detyrosinated tubulin alpha-1A chain
Q: Tubulin beta-4B chain
R: Detyrosinated tubulin alpha-1A chain
S: Tubulin beta-4B chain
T: Detyrosinated tubulin alpha-1A chain
U: Tubulin beta-4B chain
V: Detyrosinated tubulin alpha-1A chain
W: Tubulin beta-4B chain
X: Detyrosinated tubulin alpha-1A chain
Y: Tubulin beta-4B chain
Z: Detyrosinated tubulin alpha-1A chain
b: Tektin-2
e: Tektin-2
f: Tektin-2
g: Tektin-2
h: Tektin-2
i: Tektin-2
j: Tektin-2
k: Tektin-2
l: Tektin-2
m: Tektin-2
n: Detyrosinated tubulin alpha-1A chain
1: EF-hand domain-containing family member B
o: Tubulin beta-4B chain
p: Detyrosinated tubulin alpha-1A chain
q: Tubulin beta-4B chain
r: Detyrosinated tubulin alpha-1A chain
s: Tubulin beta-4B chain
t: Detyrosinated tubulin alpha-1A chain
u: Tubulin beta-4B chain
v: Detyrosinated tubulin alpha-1A chain
w: Tubulin beta-4B chain
x: Detyrosinated tubulin alpha-1A chain
y: Tubulin beta-4B chain
z: Detyrosinated tubulin alpha-1A chain
AC: Tektin-3
AD: Tektin-3
AE: Tektin-3
AF: Tektin-3
AG: Tektin-3
AH: Tektin-3
AI: Tektin-3
AJ: Tektin-3
AK: Tektin-3
a: Meiosis-specific nuclear structural protein 1
BQ: Detyrosinated tubulin alpha-1A chain
BR: Tubulin beta-4B chain
BS: Detyrosinated tubulin alpha-1A chain
BT: Tubulin beta-4B chain
2: EF-hand domain-containing family member B
BU: Detyrosinated tubulin alpha-1A chain
BV: Tubulin beta-4B chain
BW: Detyrosinated tubulin alpha-1A chain
BX: Tubulin beta-4B chain
BY: Detyrosinated tubulin alpha-1A chain
BZ: Tubulin beta-4B chain
AV: Tubulin beta-4B chain
AW: Detyrosinated tubulin alpha-1A chain
AX: Tubulin beta-4B chain
AY: Detyrosinated tubulin alpha-1A chain
Aa: Tektin-4
Ab: Tektin-4
Ac: Tektin-4
Ad: Tektin-4
Af: Tektin-4
Ag: Tektin-4
Ah: Tektin-4
Ai: Tektin-4
Aj: Detyrosinated tubulin alpha-1A chain
Ak: Tubulin beta-4B chain
Al: Detyrosinated tubulin alpha-1A chain
Am: Tubulin beta-4B chain
An: Detyrosinated tubulin alpha-1A chain
Ao: Tubulin beta-4B chain
Ap: Detyrosinated tubulin alpha-1A chain
3: Cilia- and flagella-associated protein 53
Aq: Tubulin beta-4B chain
Ar: Detyrosinated tubulin alpha-1A chain
As: Tubulin beta-4B chain
At: Detyrosinated tubulin alpha-1A chain
Au: Tubulin beta-4B chain
Av: Detyrosinated tubulin alpha-1A chain
Aw: Tubulin beta-4B chain
Az: Tektin bundle-interacting protein 1
A1: Tektin bundle-interacting protein 1
A2: Tektin bundle-interacting protein 1
A3: Tektin bundle-interacting protein 1
A4: Tubulin beta-4B chain
A5: Detyrosinated tubulin alpha-1A chain
A6: Tubulin beta-4B chain
A7: Detyrosinated tubulin alpha-1A chain
A8: Tubulin beta-4B chain
A9: Detyrosinated tubulin alpha-1A chain
A0: Tubulin beta-4B chain
BA: Detyrosinated tubulin alpha-1A chain
BB: Tubulin beta-4B chain
BC: Detyrosinated tubulin alpha-1A chain
BD: Tubulin beta-4B chain
BE: Detyrosinated tubulin alpha-1A chain
BF: Tubulin beta-4B chain
BI: Tektin-3
BJ: Tektin-3
4: Cilia- and flagella-associated protein 53
BK: Tektin-3
BL: Tektin-3
BM: Tektin-3
BN: Tubulin beta-4B chain
BO: Detyrosinated tubulin alpha-1A chain
BP: Tubulin beta-4B chain
AB: Cilia- and flagella-associated protein 141
CX: Detyrosinated tubulin alpha-1A chain
CY: Tubulin beta-4B chain
Cb: Tubulin beta-4B chain
Cc: Detyrosinated tubulin alpha-1A chain
Cd: Tubulin beta-4B chain
Ce: Detyrosinated tubulin alpha-1A chain
Cf: Tubulin beta-4B chain
Cg: Detyrosinated tubulin alpha-1A chain
Ch: Tubulin beta-4B chain
Ci: Detyrosinated tubulin alpha-1A chain
Bb: Tubulin beta-4B chain
Bc: Detyrosinated tubulin alpha-1A chain
Bd: Tubulin beta-4B chain
Be: Detyrosinated tubulin alpha-1A chain
Bf: Tubulin beta-4B chain
Bg: Detyrosinated tubulin alpha-1A chain
Bh: Tubulin beta-4B chain
Bi: Detyrosinated tubulin alpha-1A chain
Bj: Tubulin beta-4B chain
5: Nucleoside diphosphate kinase 7
Bk: Detyrosinated tubulin alpha-1A chain
Bl: Tubulin beta-4B chain
Bm: Detyrosinated tubulin alpha-1A chain
Bn: Tubulin beta-4B chain
Br: Detyrosinated tubulin alpha-1A chain
Bs: Tubulin beta-4B chain
Bt: Detyrosinated tubulin alpha-1A chain
Bu: Tubulin beta-4B chain
Bv: Detyrosinated tubulin alpha-1A chain
Bw: Tubulin beta-4B chain
Bx: Detyrosinated tubulin alpha-1A chain
By: Tubulin beta-4B chain
Bz: Detyrosinated tubulin alpha-1A chain
B1: Tubulin beta-4B chain
B2: Detyrosinated tubulin alpha-1A chain
B3: Tubulin beta-4B chain
B4: Detyrosinated tubulin alpha-1A chain
B6: Protein FAM166B
B7: Tubulin beta-4B chain
B8: Detyrosinated tubulin alpha-1A chain
B9: Tubulin beta-4B chain
B0: Detyrosinated tubulin alpha-1A chain
CA: Tubulin beta-4B chain
CB: Detyrosinated tubulin alpha-1A chain
CC: Tubulin beta-4B chain
CD: Detyrosinated tubulin alpha-1A chain
6: Nucleoside diphosphate kinase 7
CE: Tubulin beta-4B chain
CF: Detyrosinated tubulin alpha-1A chain
CG: Tubulin beta-4B chain
CH: Detyrosinated tubulin alpha-1A chain
CI: Tubulin beta-4B chain
CJ: Detyrosinated tubulin alpha-1A chain
CM: Tubulin beta-4B chain
CN: Detyrosinated tubulin alpha-1A chain
CO: Tubulin beta-4B chain
CP: Detyrosinated tubulin alpha-1A chain
CQ: Tubulin beta-4B chain
CR: Detyrosinated tubulin alpha-1A chain
CS: Tubulin beta-4B chain
CT: Detyrosinated tubulin alpha-1A chain
CU: Tubulin beta-4B chain
CV: Detyrosinated tubulin alpha-1A chain
CW: Tubulin beta-4B chain
AZ: Sperm-associated antigen 8
Di: Tubulin beta-4B chain
Dj: Detyrosinated tubulin alpha-1A chain
Dk: Tubulin beta-4B chain
Dl: Detyrosinated tubulin alpha-1A chain
Dm: Tubulin beta-4B chain
Do: RIB43A-like with coiled-coils protein 2
Dp: Detyrosinated tubulin alpha-1A chain
Dq: Tubulin beta-4B chain
7: Cilia- and flagella-associated protein 95
Dr: Detyrosinated tubulin alpha-1A chain
Ds: Tubulin beta-4B chain
Cj: Tubulin beta-4B chain
Ck: Detyrosinated tubulin alpha-1A chain
Cl: Tubulin beta-4B chain
Cm: Detyrosinated tubulin alpha-1A chain
Cn: Tubulin beta-4B chain
Co: Detyrosinated tubulin alpha-1A chain
Cr: Tubulin beta-4B chain
Cs: Detyrosinated tubulin alpha-1A chain
Ct: Tubulin beta-4B chain
Cu: Detyrosinated tubulin alpha-1A chain
Cv: Tubulin beta-4B chain
Cw: Detyrosinated tubulin alpha-1A chain
Cx: Tubulin beta-4B chain
Cy: Detyrosinated tubulin alpha-1A chain
Cz: Tubulin beta-4B chain
C1: Detyrosinated tubulin alpha-1A chain
C2: Tubulin beta-4B chain
C3: Detyrosinated tubulin alpha-1A chain
C4: Tubulin beta-4B chain
C7: Tubulin beta-4B chain
C8: Detyrosinated tubulin alpha-1A chain
C9: Tubulin beta-4B chain
C0: Detyrosinated tubulin alpha-1A chain
DA: Tubulin beta-4B chain
8: Cilia- and flagella-associated protein 107
DB: Detyrosinated tubulin alpha-1A chain
DC: Tubulin beta-4B chain
DD: Detyrosinated tubulin alpha-1A chain
DE: Tubulin beta-4B chain
DF: Detyrosinated tubulin alpha-1A chain
DG: Tubulin beta-4B chain
DH: Detyrosinated tubulin alpha-1A chain
DI: Tubulin beta-4B chain
DL: Tubulin beta-4B chain
DM: Detyrosinated tubulin alpha-1A chain
DN: Tubulin beta-4B chain
DO: Detyrosinated tubulin alpha-1A chain
DP: Tubulin beta-4B chain
DQ: Detyrosinated tubulin alpha-1A chain
DR: Tubulin beta-4B chain
DS: Detyrosinated tubulin alpha-1A chain
DT: Tubulin beta-4B chain
DU: Detyrosinated tubulin alpha-1A chain
DV: Tubulin beta-4B chain
DW: Detyrosinated tubulin alpha-1A chain
DX: Tubulin beta-4B chain
Db: Detyrosinated tubulin alpha-1A chain
Dc: Tubulin beta-4B chain
Dd: Detyrosinated tubulin alpha-1A chain
De: Tubulin beta-4B chain
Df: Detyrosinated tubulin alpha-1A chain
9: Cilia- and flagella-associated protein 107
Dg: Tubulin beta-4B chain
Dh: Detyrosinated tubulin alpha-1A chain
Ay: Cilia- and flagella-associated protein 161
Er: Tubulin beta-4B chain
Es: Detyrosinated tubulin alpha-1A chain
Et: Tubulin beta-4B chain
Eu: Detyrosinated tubulin alpha-1A chain
Ev: Tubulin beta-4B chain
Ew: Detyrosinated tubulin alpha-1A chain
Ex: Tubulin beta-4B chain
Ey: Detyrosinated tubulin alpha-1A chain
E1: EF-hand domain-containing protein 1
E3: Detyrosinated tubulin alpha-1A chain
Dt: Detyrosinated tubulin alpha-1A chain
Du: Tubulin beta-4B chain
Dv: Detyrosinated tubulin alpha-1A chain
Dw: Tubulin beta-4B chain
Dx: Detyrosinated tubulin alpha-1A chain
Dy: Tubulin beta-4B chain
Dz: Detyrosinated tubulin alpha-1A chain
D1: Tubulin beta-4B chain
D2: Detyrosinated tubulin alpha-1A chain
D5: Detyrosinated tubulin alpha-1A chain
D6: Tubulin beta-4B chain
D7: Detyrosinated tubulin alpha-1A chain
D8: Tubulin beta-4B chain
A: Meiosis-specific nuclear structural protein 1
D9: Detyrosinated tubulin alpha-1A chain
D0: Tubulin beta-4B chain
EA: Detyrosinated tubulin alpha-1A chain
EB: Tubulin beta-4B chain
EC: Detyrosinated tubulin alpha-1A chain
ED: Tubulin beta-4B chain
EE: Detyrosinated tubulin alpha-1A chain
EF: Tubulin beta-4B chain
EG: Detyrosinated tubulin alpha-1A chain
EJ: Detyrosinated tubulin alpha-1A chain
EK: Tubulin beta-4B chain
EL: Detyrosinated tubulin alpha-1A chain
EM: Tubulin beta-4B chain
EN: Detyrosinated tubulin alpha-1A chain
EO: Tubulin beta-4B chain
EP: Detyrosinated tubulin alpha-1A chain
EQ: Tubulin beta-4B chain
ER: Detyrosinated tubulin alpha-1A chain
ES: Tubulin beta-4B chain
ET: Detyrosinated tubulin alpha-1A chain
EU: Tubulin beta-4B chain
EV: Detyrosinated tubulin alpha-1A chain
EY: Detyrosinated tubulin alpha-1A chain
EZ: Tubulin beta-4B chain
Ea: Detyrosinated tubulin alpha-1A chain
Eb: Tubulin beta-4B chain
AL: Tektin-3
Ec: Detyrosinated tubulin alpha-1A chain
Ed: Tubulin beta-4B chain
Ee: Detyrosinated tubulin alpha-1A chain
Ef: Tubulin beta-4B chain
Eg: Detyrosinated tubulin alpha-1A chain
Eh: Tubulin beta-4B chain
Ei: Detyrosinated tubulin alpha-1A chain
Ej: Tubulin beta-4B chain
Ek: Detyrosinated tubulin alpha-1A chain
Em: EF-hand domain-containing protein 1
Eo: Detyrosinated tubulin alpha-1A chain
Ep: Tubulin beta-4B chain
Eq: Detyrosinated tubulin alpha-1A chain
BH: Cilia- and flagella-associated protein 161
F1: Sperm acrosome-associated protein 9
F2: Sperm acrosome-associated protein 9
F3: Sperm acrosome-associated protein 9
F4: Sperm acrosome-associated protein 9
F5: Sperm acrosome-associated protein 9
F6: Sperm acrosome-associated protein 9
F7: Sperm acrosome-associated protein 9
F8: Sperm acrosome-associated protein 9
F9: Sperm acrosome-associated protein 9
F0: Sperm acrosome-associated protein 9
E4: Tubulin beta-4B chain
E5: Detyrosinated tubulin alpha-1A chain
AM: Detyrosinated tubulin alpha-1A chain
E6: Tubulin beta-4B chain
E7: Detyrosinated tubulin alpha-1A chain
E8: Tubulin beta-4B chain
E9: Detyrosinated tubulin alpha-1A chain
E0: Tubulin beta-4B chain
FA: Detyrosinated tubulin alpha-1A chain
FB: Tubulin beta-4B chain
FC: Detyrosinated tubulin alpha-1A chain
FD: Tubulin beta-4B chain
FE: EF-hand domain-containing protein 1
FG: Detyrosinated tubulin alpha-1A chain
FH: Tubulin beta-4B chain
FI: Detyrosinated tubulin alpha-1A chain
FJ: Tubulin beta-4B chain
FK: Detyrosinated tubulin alpha-1A chain
FL: Tubulin beta-4B chain
FM: Detyrosinated tubulin alpha-1A chain
FN: Tubulin beta-4B chain
FO: Detyrosinated tubulin alpha-1A chain
FP: Tubulin beta-4B chain
FQ: Detyrosinated tubulin alpha-1A chain
FR: Tubulin beta-4B chain
FU: Detyrosinated tubulin alpha-1A chain
FV: Tubulin beta-4B chain
FW: Detyrosinated tubulin alpha-1A chain
FX: Tubulin beta-4B chain
AN: Tubulin beta-4B chain
FY: Detyrosinated tubulin alpha-1A chain
FZ: Tubulin beta-4B chain
Fa: Detyrosinated tubulin alpha-1A chain
Fb: Tubulin beta-4B chain
Fc: Detyrosinated tubulin alpha-1A chain
Fd: Tubulin beta-4B chain
Fe: Detyrosinated tubulin alpha-1A chain
Ff: Tubulin beta-4B chain
Fg: EF-hand domain-containing family member C2
Fh: Cilia- and flagella-associated protein 20
Fi: Cilia- and flagella-associated protein 20
Fj: Cilia- and flagella-associated protein 20
Fk: Cilia- and flagella-associated protein 20
Fl: Cilia- and flagella-associated protein 20
Fm: Cilia- and flagella-associated protein 20
Fn: Cilia- and flagella-associated protein 20
Fp: Parkin coregulated gene protein homolog
Fq: Parkin coregulated gene protein homolog
Fr: Parkin coregulated gene protein homolog
Fs: Parkin coregulated gene protein homolog
Ft: Parkin coregulated gene protein homolog
Fx: Dual specificity protein phosphatase 3
Fy: Dual specificity protein phosphatase 3
Fz: Dual specificity protein phosphatase 3
G: Piercer of microtubule wall 2 protein
GA: Sperm acrosome-associated protein 9
AO: Detyrosinated tubulin alpha-1A chain
GB: Sperm acrosome-associated protein 9
GC: Sperm acrosome-associated protein 9
GD: Sperm acrosome-associated protein 9
GE: Sperm acrosome-associated protein 9
GF: Sperm acrosome-associated protein 9
GG: Sperm acrosome-associated protein 9
GH: Sperm acrosome-associated protein 9
GI: Sperm acrosome-associated protein 9
GJ: Sperm acrosome-associated protein 9
GK: Sperm acrosome-associated protein 9
GL: Sperm acrosome-associated protein 9
GM: Sperm acrosome-associated protein 9
GN: Sperm acrosome-associated protein 9
GO: Sperm acrosome-associated protein 9
GP: Sperm acrosome-associated protein 9
GQ: Sperm acrosome-associated protein 9
GR: Tektin-5
GS: Tektin-5
GT: Tektin-5
GU: Tektin-5
GV: Tektin-5
GW: Tektin-5
GX: Tektin-5
GY: Tektin-5
GZ: Tektin-5
Ga: Tektin-5
AP: Tubulin beta-4B chain
Gb: Tektin-5
Gc: Tektin-5
Gd: Tektin-5
Ge: Tektin-5
z0: Tektin-5
z1: Tektin-5
z3: Tektin-5
z4: Tektin-5
Gf: Tektin-5
Gg: Tektin-5
Gh: Tektin-5
Gi: Tektin-5
Gj: Tektin-5
Bq: Tubulin beta-4B chain
CL: Protein FAM166B
Ca: Protein FAM166B
Cq: Protein FAM166B
C6: Protein FAM166B
DK: Protein FAM166B
Da: Tubulin beta-4B chain
DZ: RIB43A-like with coiled-coils protein 2
D4: RIB43A-like with coiled-coils protein 2
EI: RIB43A-like with coiled-coils protein 2
EX: RIB43A-like with coiled-coils protein 2
AQ: Detyrosinated tubulin alpha-1A chain
En: Tubulin beta-4B chain
E2: Tubulin beta-4B chain
FF: Tubulin beta-4B chain
FT: Tubulin beta-4B chain
FS: EF-hand domain-containing family member C2
Fo: EF-hand domain-containing family member C2
Fv: EF-hand domain-containing family member C2
B: Cilia- and flagella-associated protein 45
AA: Cilia- and flagella-associated protein 45
c: Cilia- and flagella-associated protein 45
Ax: Cilia- and flagella-associated protein 45
BG: Cilia- and flagella-associated protein 52
Ba: Cilia- and flagella-associated protein 52
Bo: Cilia- and flagella-associated protein 52
B5: Enkurin
CK: Enkurin
CZ: Enkurin
Cp: Enkurin
C5: Protein Flattop
DJ: Protein Flattop
DY: Protein Flattop
Dn: Cilia- and flagella- associated protein 210
D3: Cilia- and flagella- associated protein 210
EH: Cilia- and flagella-associated protein 276
EW: Cilia- and flagella-associated protein 276
El: Cilia- and flagella-associated protein 276
AR: Tubulin beta-4B chain
Ez: EF-hand calcium-binding domain-containing protein 6
d: Cilia- and flagella-associated protein 45
C: Coiled-coil domain-containing protein 105
D: Coiled-coil domain-containing protein 105
E: Coiled-coil domain-containing protein 105
Fw: Piercer of microtubule wall 1 protein
AS: Detyrosinated tubulin alpha-1A chain
AT: Tubulin beta-4B chain
AU: Detyrosinated tubulin alpha-1A chain
F: Coiled-coil domain-containing protein 105
H: Coiled-coil domain-containing protein 105
I: Tektin-1
J: Tektin-1
K: Tektin-1


Theoretical massNumber of molelcules
Total (without water)22,692,158471
Polymers22,692,158471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Cilia- and flagella-associated protein ... , 9 types, 27 molecules 0734AB89AyBHFhFiFjFkFlFmFnBAAcAxdBGBaBoEHEWEl

#1: Protein Cilia- and flagella-associated protein 95


Mass: 26633.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQC3
#10: Protein Cilia- and flagella-associated protein 53


Mass: 62036.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D439
#12: Protein Cilia- and flagella-associated protein 141


Mass: 12278.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9D9
#17: Protein Cilia- and flagella-associated protein 107


Mass: 23062.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q4KKZ1
#18: Protein Cilia- and flagella-associated protein 161


Mass: 34433.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P8Y0
#22: Protein
Cilia- and flagella-associated protein 20 / Gene trap locus 3 protein


Mass: 22781.389 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BTU1
#27: Protein
Cilia- and flagella-associated protein 45


Mass: 65962.016 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9U9
#28: Protein Cilia- and flagella-associated protein 52 / WD repeat-containing protein 16


Mass: 68322.164 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5F201
#32: Protein Cilia- and flagella-associated protein 276


Mass: 18960.092 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAD0

+
Protein , 22 types, 436 molecules LMIJKNPRTVXZnprtvxzBQBSBUBWBYAWAYAjAlAnAp...

#2: Protein
Tektin-1 /


Mass: 48713.035 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAJ2
#3: Protein ...
Detyrosinated tubulin alpha-1A chain


Mass: 50188.441 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68369
#4: Protein ...
Tubulin beta-4B chain / / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372
#5: Protein
Tektin-2 / / Tektin-t / Testicular tektin


Mass: 50385.066 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q922G7
#7: Protein
Tektin-3 /


Mass: 56754.777 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6X6Z7
#8: Protein Meiosis-specific nuclear structural protein 1


Mass: 60353.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q61884
#9: Protein
Tektin-4 /


Mass: 52121.449 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q149S1
#11: Protein
Tektin bundle-interacting protein 1


Mass: 23987.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A6H6Q4
#13: Protein Nucleoside diphosphate kinase 7 / Nucleoside-diphosphate kinase / NDK 7 / NDP kinase 7 / nm23-M7


Mass: 44489.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9QXL8, nucleoside-diphosphate kinase
#14: Protein
Protein FAM166B


Mass: 30290.346 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2AIP0
#15: Protein Sperm-associated antigen 8 / / Sperm membrane protein 1 / SMP-1 / Sperm membrane protein BS-84


Mass: 50591.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3V0Q6
#16: Protein
RIB43A-like with coiled-coils protein 2


Mass: 45328.156 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4Q1
#19: Protein EF-hand domain-containing protein 1 / Myoclonin-1


Mass: 75235.422 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9T8
#20: Protein ...
Sperm acrosome-associated protein 9 / Acrosome and sperm tail protein / MAST


Mass: 19512.373 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TPM5
#23: Protein
Parkin coregulated gene protein homolog / Hypertension-related protein 1-like protein / PARK2 coregulated gene protein


Mass: 27763.268 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAK2
#24: Protein Dual specificity protein phosphatase 3 / T-DSP11 / Vaccinia H1-related phosphatase / VHR


Mass: 20494.127 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9D7X3, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#26: Protein ...
Tektin-5 /


Mass: 62817.535 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G5E8A8
#29: Protein
Enkurin /


Mass: 29587.521 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6SP97
#30: Protein Protein Flattop


Mass: 20575.123 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P8X9
#31: Protein Cilia- and flagella- associated protein 210


Mass: 65266.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0JLY1
#33: Protein EF-hand calcium-binding domain-containing protein 6 / DJ-1-binding protein / DJBP


Mass: 176028.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P1E8
#34: Protein
Coiled-coil domain-containing protein 105


Mass: 57406.484 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4K7

-
EF-hand domain-containing family member ... , 2 types, 6 molecules 12FgFSFoFv

#6: Protein EF-hand domain-containing family member B / Cilia- and flagella-associated protein 21


Mass: 95891.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8CDU5
#21: Protein
EF-hand domain-containing family member C2


Mass: 87758.023 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D485

-
Piercer of microtubule wall ... , 2 types, 2 molecules GFw

#25: Protein Piercer of microtubule wall 2 protein


Mass: 13728.513 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: V9GXK1
#35: Protein Piercer of microtubule wall 1 protein / Pierce1 / p53-induced expression in RB-null cells protein 1


Mass: 18862.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5BN45

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Mouse sperm / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 4 e/Å2 / Avg electron dose per subtomogram: 100 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: RELION / Version: 4.0-beta2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12848 / Symmetry type: POINT
EM volume selectionDetails: 32288 particles were initially picked every 24 nm along the microtubules.
Num. of tomograms: 76 / Num. of volumes extracted: 32288

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