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- PDB-7kek: Structure of the free outer-arm dynein in pre-parallel state -

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Basic information

Entry
Database: PDB / ID: 7kek
TitleStructure of the free outer-arm dynein in pre-parallel state
Components
  • (Dynein intermediate chain ...) x 2
  • (Dynein light chain ...) x 11
  • Dynein alpha heavy chain
  • Dynein beta heavy chain
  • Dynein gamma heavy chain
  • Thioredoxin LC3BL
KeywordsMOTOR PROTEIN / OAD / axonemal / pre-paralle
Function / homology
Function and homology information


dynein complex / minus-end-directed microtubule motor activity / 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
Kelch motif / Galactose oxidase, central domain / 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 ...Kelch motif / Galactose oxidase, central domain / 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 / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / 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 / IPT/TIG domain / Kelch-type beta propeller / Leucine-rich repeat, SDS22-like subfamily / ig-like, plexins, transcription factors / Thioredoxin / IPT domain / Leucine-rich repeat profile. / Thioredoxin domain / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / 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 / Immunoglobulin-like fold / 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 / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Outer arm dynein beta heavy chain / Dynein light chain roadblock-type 2 protein / Dynein light chain / Dynein light chain ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Thioredoxin / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / 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 2A / Dynein light chain 1 / Dynein heavy chain, outer arm protein / Dynein light chain roadblock-type 2 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: 8 Å
AuthorsRao, Q. / Zhang, K.
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
DepositionOct 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Dynein alpha heavy chain
C: Dynein gamma heavy chain
Q: Dynein light chain 1
B: Dynein beta heavy chain
I: Dynein light chain LC8_1a (LC10)
H: Dynein light chain LC8_1b (DLC82)
G: Dynein light chain roadblock LC7B
F: Dynein light chain roadblock LC7A
N: Dynein light chain Tctex_b
O: Dynein light chain Tctex_a (LC2A)
E: Dynein intermediate chain DIC3
D: Dynein intermediate chain DIC2
P: Thioredoxin LC3BL
L: Dynein light chain LC8_3b
K: Dynein light chain LC8_2a (LC8E)
J: Dynein light chain LC8_2b
M: Dynein light chain LC8_3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,869,07635
Polymers1,864,77317
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 , 3 types, 3 molecules ACP

#1: Protein Dynein alpha heavy chain


Mass: 534400.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22A67
#2: Protein Dynein gamma heavy chain


Mass: 475554.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M6H4
#13: Protein Thioredoxin LC3BL


Mass: 14256.472 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 chain ... , 11 types, 11 molecules QIHGFNOLKJM

#3: Protein Dynein light chain 1


Mass: 22851.654 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 LC8_1a (LC10)


Mass: 12348.086 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 LC8_1b (DLC82)


Mass: 10780.357 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 LC7B


Mass: 18490.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22MV2
#8: Protein Dynein light chain roadblock LC7A


Mass: 14751.817 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_b


Mass: 13202.817 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 Tctex_a (LC2A)


Mass: 15608.120 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 LC8_3b


Mass: 12516.457 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 LC8_2a (LC8E)


Mass: 10973.408 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 LC8_2b


Mass: 13336.089 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 LC8_3a


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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Dynein intermediate chain ... , 2 types, 2 molecules ED

#11: Protein Dynein intermediate chain DIC3


Mass: 77178.062 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 DIC2


Mass: 77888.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M008

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Antibody , 1 types, 1 molecules B

#4: Antibody Dynein beta heavy chain


Mass: 530182.375 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Free outer-arm dynein / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 53.3 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209656 / Symmetry type: POINT

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