7N32 | pdb_00007n32

protofilaments of microtubule doublets bound to outer-arm dynein

PDB DOI: https://doi.org/10.2210/pdb7N32/pdb
EM Map EMD-22677: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Tetrahymena thermophila
Mutation(s): No

Deposited: 2021-05-31 Released: 2021-09-29
Deposition Author(s): Rao, Q., Zhang, K.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism.

Rao, Q., Han, L., Wang, Y., Chai, P., Kuo, Y.W., Yang, R., Hu, F., Yang, Y., Howard, J., Zhang, K.

(2021) Nat Struct Mol Biol 28: 799-810

PubMed: 34556869 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-021-00656-9
Primary Citation Related Structures:
7K58, 7K5B, 7KEK, 7MWG, 7N32

PubMed 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 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.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Macromolecule Content

Total Structure Weight: 1,202.53 kDa
Atom Count: 82,021
Modeled Residue Count: 10,460
Deposited Residue Count: 10,704
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A [auth w] C [auth u] E [auth s] G [auth q] I [auth o] A [auth w], C [auth u], E [auth s], G [auth q], I [auth o], K [auth m], M [auth k], O [auth g], Q [auth e], S [auth c], T [auth a], W [auth i]	449	Tetrahymena thermophila	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P41351 (Tetrahymena thermophila) Explore P41351 Go to UniProtKB: P41351
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41351
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B [auth x] D [auth v] F [auth t] H [auth r] J [auth p] B [auth x], D [auth v], F [auth t], H [auth r], J [auth p], L [auth n], N [auth l], P [auth h], R [auth f], U [auth b], V [auth d], X [auth j]	443	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for P41352 (Tetrahymena thermophila) Explore P41352 Go to UniProtKB: P41352
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41352
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain ZA [auth c] SDF format, chain Y [auth w] SDF format, chain WA [auth e] SDF format, chain TA [auth g] SDF format, chain QA [auth k] SDF format, chain NA [auth m] SDF format, chain KA [auth o] SDF format, chain HA [auth q] SDF format, chain EB [auth i] SDF format, chain EA [auth s] SDF format, chain BB [auth a] SDF format, chain BA [auth u] MOL2 format, chain ZA [auth c] MOL2 format, chain Y [auth w] MOL2 format, chain WA [auth e] MOL2 format, chain TA [auth g] MOL2 format, chain QA [auth k] MOL2 format, chain NA [auth m] MOL2 format, chain KA [auth o] MOL2 format, chain HA [auth q] MOL2 format, chain EB [auth i] MOL2 format, chain EA [auth s] MOL2 format, chain BB [auth a] MOL2 format, chain BA [auth u] mmCIF format, chain ZA [auth c] mmCIF format, chain Y [auth w] mmCIF format, chain WA [auth e] mmCIF format, chain TA [auth g] mmCIF format, chain QA [auth k] mmCIF format, chain NA [auth m] mmCIF format, chain KA [auth o] mmCIF format, chain HA [auth q] mmCIF format, chain EB [auth i] mmCIF format, chain EA [auth s] mmCIF format, chain BB [auth a] mmCIF format, chain BA [auth u]	BA [auth u] BB [auth a] EA [auth s] EB [auth i] HA [auth q] BA [auth u], BB [auth a], EA [auth s], EB [auth i], HA [auth q], KA [auth o], NA [auth m], QA [auth k], TA [auth g], WA [auth e], Y [auth w], ZA [auth c]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain BA [auth u] Focus chain BB [auth a] Focus chain EA [auth s] Focus chain EB [auth i] Focus chain HA [auth q] Focus chain KA [auth o] Focus chain NA [auth m] Focus chain QA [auth k] Focus chain TA [auth g] Focus chain WA [auth e] Focus chain Y [auth w] Focus chain ZA [auth c] Interactions & Density Focus chain BA [auth u] Focus chain BB [auth a] Focus chain EA [auth s] Focus chain EB [auth i] Focus chain HA [auth q] Focus chain KA [auth o] Focus chain NA [auth m] Focus chain QA [auth k] Focus chain TA [auth g] Focus chain WA [auth e] Focus chain Y [auth w] Focus chain ZA [auth c]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain YA [auth f] SDF format, chain VA [auth h] SDF format, chain SA [auth l] SDF format, chain PA [auth n] SDF format, chain MA [auth p] SDF format, chain JA [auth r] SDF format, chain GB [auth j] SDF format, chain GA [auth t] SDF format, chain DB [auth b] SDF format, chain DA [auth v] SDF format, chain AA [auth x] MOL2 format, chain YA [auth f] MOL2 format, chain VA [auth h] MOL2 format, chain SA [auth l] MOL2 format, chain PA [auth n] MOL2 format, chain MA [auth p] MOL2 format, chain JA [auth r] MOL2 format, chain GB [auth j] MOL2 format, chain GA [auth t] MOL2 format, chain DB [auth b] MOL2 format, chain DA [auth v] MOL2 format, chain AA [auth x] mmCIF format, chain YA [auth f] mmCIF format, chain VA [auth h] mmCIF format, chain SA [auth l] mmCIF format, chain PA [auth n] mmCIF format, chain MA [auth p] mmCIF format, chain JA [auth r] mmCIF format, chain GB [auth j] mmCIF format, chain GA [auth t] mmCIF format, chain DB [auth b] mmCIF format, chain DA [auth v] mmCIF format, chain AA [auth x]	AA [auth x] DA [auth v] DB [auth b] GA [auth t] GB [auth j] AA [auth x], DA [auth v], DB [auth b], GA [auth t], GB [auth j], JA [auth r], MA [auth p], PA [auth n], SA [auth l], VA [auth h], YA [auth f]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain AA [auth x] Focus chain DA [auth v] Focus chain DB [auth b] Focus chain GA [auth t] Focus chain GB [auth j] Focus chain JA [auth r] Focus chain MA [auth p] Focus chain PA [auth n] Focus chain SA [auth l] Focus chain VA [auth h] Focus chain YA [auth f] Interactions & Density Focus chain AA [auth x] Focus chain DA [auth v] Focus chain DB [auth b] Focus chain GA [auth t] Focus chain GB [auth j] Focus chain JA [auth r] Focus chain MA [auth p] Focus chain PA [auth n] Focus chain SA [auth l] Focus chain VA [auth h] Focus chain YA [auth f]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth x] SDF format, chain XA [auth e] SDF format, chain UA [auth g] SDF format, chain RA [auth k] SDF format, chain OA [auth m] SDF format, chain LA [auth o] SDF format, chain IA [auth q] SDF format, chain FB [auth i] SDF format, chain FA [auth t] SDF format, chain CB [auth a] SDF format, chain CA [auth u] SDF format, chain AB [auth c] MOL2 format, chain Z [auth x] MOL2 format, chain XA [auth e] MOL2 format, chain UA [auth g] MOL2 format, chain RA [auth k] MOL2 format, chain OA [auth m] MOL2 format, chain LA [auth o] MOL2 format, chain IA [auth q] MOL2 format, chain FB [auth i] MOL2 format, chain FA [auth t] MOL2 format, chain CB [auth a] MOL2 format, chain CA [auth u] MOL2 format, chain AB [auth c] mmCIF format, chain Z [auth x] mmCIF format, chain XA [auth e] mmCIF format, chain UA [auth g] mmCIF format, chain RA [auth k] mmCIF format, chain OA [auth m] mmCIF format, chain LA [auth o] mmCIF format, chain IA [auth q] mmCIF format, chain FB [auth i] mmCIF format, chain FA [auth t] mmCIF format, chain CB [auth a] mmCIF format, chain CA [auth u] mmCIF format, chain AB [auth c]	AB [auth c] CA [auth u] CB [auth a] FA [auth t] FB [auth i] AB [auth c], CA [auth u], CB [auth a], FA [auth t], FB [auth i], IA [auth q], LA [auth o], OA [auth m], RA [auth k], UA [auth g], XA [auth e], Z [auth x]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth c] Focus chain CA [auth u] Focus chain CB [auth a] Focus chain FA [auth t] Focus chain FB [auth i] Focus chain IA [auth q] Focus chain LA [auth o] Focus chain OA [auth m] Focus chain RA [auth k] Focus chain UA [auth g] Focus chain XA [auth e] Focus chain Z [auth x] Interactions & Density Focus chain AB [auth c] Focus chain CA [auth u] Focus chain CB [auth a] Focus chain FA [auth t] Focus chain FB [auth i] Focus chain IA [auth q] Focus chain LA [auth o] Focus chain OA [auth m] Focus chain RA [auth k] Focus chain UA [auth g] Focus chain XA [auth e] Focus chain Z [auth x]