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- PDB-7k5b: Structure of outer-arm dynein bound to microtubule doublet in mic... -

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Basic information

Entry
Database: PDB / ID: 7k5b
TitleStructure of outer-arm dynein bound to microtubule doublet in microtubule binding state 2 (MTBS-2)
Components
  • (Dynein light ...) x 12
  • 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
KeywordsMOTOR PROTEIN / three head / outer dynein arms / microtubule binding
Function / homology
Function and homology information


axonemal dynein complex / outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / dynein complex / myosin II complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex ...axonemal dynein complex / outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / dynein complex / myosin II complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / microtubule-based movement / dynein intermediate chain binding / microtubule-based process / cell projection / microtubule / cilium / calcium ion binding / ATP binding / cytoplasm
Similarity search - Function
: / Dynein heavy chain 3, AAA+ lid domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / AAA+ lid domain / : / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 ...: / Dynein heavy chain 3, AAA+ lid domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / AAA+ lid domain / : / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / EF hand domain / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / 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 / 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 / : / Thioredoxin domain / Leucine-rich repeat profile. / Leucine-rich repeat / EF-hand domain pair / Leucine-rich repeat domain superfamily / 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 / WD domain, G-beta repeat / Thioredoxin-like superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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 / Dynein-1, subspecies f / 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 / Dynein-1, subspecies f / Dynein light chain roadblock-type 2 protein / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain 4A / Dynein light chain 2A / Dynein axonemal 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: 4.5 Å
AuthorsRao, Q. / Zhang, K.
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
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Dynein heavy chain, outer arm protein
B: Outer arm dynein beta heavy chain
C: gamma heavy chain
D: Dynein intermediate chain 2
E: Flagellar outer dynein arm intermediate protein, putative
F: Dynein light chain roadblock-type 2 protein
G: Dynein light chain roadblock-type 2 protein
H: Dynein light chain
I: Dynein light chain
J: Dynein light chain
K: Dynein light chain
L: Dynein light chain
M: Dynein light chain
N: Dynein light chain tctex-type 1 protein
O: Dynein light chain 2A
P: Thioredoxin
Q: Dynein light chain 1
R: Dynein light chain 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,828,82036
Polymers1,824,51618
Non-polymers4,30318
Water00
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 ACDEP

#1: Protein Dynein heavy chain, outer arm protein


Mass: 533780.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22A67
#3: Protein gamma heavy chain


Mass: 450623.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#4: 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
#5: 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
#16: 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 ... , 12 types, 12 molecules FGHIJKLMNOQR

#6: Protein Dynein light chain roadblock-type 2 protein


Mass: 14193.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MHB1
#7: Protein Dynein light chain roadblock-type 2 protein


Mass: 17470.111 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


Mass: 10649.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFW2
#9: 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
#10: Protein Dynein light chain


Mass: 11435.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22R86
#11: 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
#12: Protein Dynein light chain


Mass: 12516.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7XJB1
#13: 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
#14: Protein Dynein light chain tctex-type 1 protein


Mass: 12856.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VEB3
#15: 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
#17: Protein Dynein light chain 1


Mass: 21705.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HGH9
#18: Protein Dynein light chain 4A


Mass: 16803.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q1HFX4

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Antibody , 1 types, 1 molecules B

#2: Antibody Outer arm dynein beta heavy chain


Mass: 529207.188 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

#19: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#21: 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
Has protein modificationY

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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 bound to microtubule doublet in microtubule binding state 2 (MTBS-2)
Type: COMPLEX / Entity ID: #1-#18 / 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 FIELD
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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76936 / Symmetry type: POINT

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