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- PDB-7k58: Structure of outer-arm dyneins bound to microtubule with microtub... -

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Basic information

Entry
Database: PDB / ID: 7k58
TitleStructure of outer-arm dyneins bound to microtubule with microtubule binding state 1(MTBS-1)
Components
  • (Dynein light ...) x 11
  • Dynein heavy chain, outer arm protein
  • Dynein intermediate chain 2
  • Flagellar outer dynein arm intermediate protein, putative
  • Outer arm dynein beta heavy chain
  • Thioredoxin
  • gamma heavy chain
KeywordsSTRUCTURAL PROTEIN / outer-arm dynein / axonemal dynein / microtubule doublet
Function / homology
Function and homology information


dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / microtubule / ATP hydrolysis activity ...dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Dynein light chain roadblock-type 1/2 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain ...Dynein light chain roadblock-type 1/2 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Leucine-rich repeat, SDS22-like subfamily / Thioredoxin / Leucine-rich repeat profile. / Thioredoxin domain / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Thioredoxin-like superfamily / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Thioredoxin / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Outer arm dynein beta heavy chain / Dynein light chain roadblock-type 2 protein / Dynein light chain / Dynein light chain / Dynein light chain ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Thioredoxin / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Outer arm dynein beta heavy chain / Dynein light chain roadblock-type 2 protein / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain roadblock / Dynein light chain 2A / Dynein light chain 1 / Dynein heavy chain, outer arm protein / Dynein light chain / Flagellar outer dynein arm intermediate protein, putative / Dynein light chain
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsQinhui, R. / Kai, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism.
Authors: Qinhui Rao / Long Han / Yue Wang / Pengxin Chai / Yin-Wei Kuo / Renbin Yang / Fangheng Hu / Yuchen Yang / Jonathon Howard / Kai Zhang /
Abstract: Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule ...Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule doublets (MTDs). Using electron microscopy, we determined high-resolution structures of Tetrahymena thermophila OAD arrays bound to MTDs in two different states. OAD preferentially binds to MTD protofilaments with a pattern resembling the native tracks for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. We propose that OADs in an array sequentially hydrolyze ATP to slide the MTDs. ATP hydrolysis in turn relaxes the TTH interfaces to effect free nucleotide cycles of downstream OADs. These findings lead to a model explaining how conformational changes in the axoneme produce coordinated action of dyneins.
History
DepositionSep 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Dynein heavy chain, outer arm protein
C: gamma heavy chain
Q: Dynein light chain 1
B: Outer arm dynein beta heavy chain
I: Dynein light chain
H: Dynein light chain
G: Dynein light chain roadblock
F: Dynein light chain roadblock-type 2 protein
N: Dynein light chain tctex-type 1 protein
O: Dynein light chain 2A
E: Flagellar outer dynein arm intermediate protein, putative
D: Dynein intermediate chain 2
P: Thioredoxin
L: Dynein light chain
K: Dynein light chain
J: Dynein light chain
M: Dynein light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,801,66635
Polymers1,797,36317
Non-polymers4,30318
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules ACEDP

#1: Protein Dynein heavy chain, outer arm protein


Mass: 533781.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22A67
#2: Protein gamma heavy chain /


Mass: 450151.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#11: Protein Flagellar outer dynein arm intermediate protein, putative


Mass: 63702.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23FU1
#12: Protein Dynein intermediate chain 2


Mass: 69514.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M008
#13: Protein Thioredoxin /


Mass: 12987.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VD75

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Dynein light ... , 11 types, 11 molecules QIHGFNOLKJM

#3: Protein Dynein light chain 1


Mass: 21737.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HGH9
#5: Protein Dynein light chain /


Mass: 11830.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFX0
#6: Protein Dynein light chain /


Mass: 10649.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFW2
#7: Protein Dynein light chain roadblock


Mass: 10741.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFX1
#8: Protein Dynein light chain roadblock-type 2 protein


Mass: 12293.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MHB1
#9: Protein Dynein light chain tctex-type 1 protein


Mass: 12899.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VEB3
#10: Protein Dynein light chain 2A


Mass: 14117.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HGH8
#14: Protein Dynein light chain /


Mass: 11108.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7XJB1
#15: Protein Dynein light chain /


Mass: 10670.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFV9
#16: Protein Dynein light chain /


Mass: 11403.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22R86
#17: Protein Dynein light chain /


Mass: 10453.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFW0

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Antibody , 1 types, 1 molecules B

#4: Antibody Outer arm dynein beta heavy chain


Mass: 529322.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M9J2

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Non-polymers , 3 types, 18 molecules

#18: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#19: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#20: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Outer-arm dynein / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: YES
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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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
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0257 / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191776 / Symmetry type: POINT
RefinementResolution: 3.5→421.23 Å / Cor.coef. Fo:Fc: 0.925 / SU B: 15.843 / SU ML: 0.24 / ESU R: 0.288
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.37379 --
obs0.37379 2900481 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 204.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.4 Å2-0.3 Å2
2---1.07 Å2-0.98 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Total: 117936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.013120083
ELECTRON MICROSCOPYr_bond_other_d0.0010.017109124
ELECTRON MICROSCOPYr_angle_refined_deg1.3461.643162539
ELECTRON MICROSCOPYr_angle_other_deg1.081.58252909
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.191515263
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.4123.6045738
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.9051520666
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.21715547
ELECTRON MICROSCOPYr_chiral_restr0.0470.216345
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02134589
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0224047
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it11.35522.60361295
ELECTRON MICROSCOPYr_mcbond_other11.35522.60361294
ELECTRON MICROSCOPYr_mcangle_it18.47633.90676477
ELECTRON MICROSCOPYr_mcangle_other18.47633.90676478
ELECTRON MICROSCOPYr_scbond_it10.70823.01758788
ELECTRON MICROSCOPYr_scbond_other10.70823.01758788
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other18.88834.10686062
ELECTRON MICROSCOPYr_long_range_B_refined27.928133463
ELECTRON MICROSCOPYr_long_range_B_other27.928133464
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.484 214605 -
obs--100 %

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