7MOQ

The structure of the Tetrahymena thermophila outer dynein arm on doublet microtubule

PDB DOI: https://doi.org/10.2210/pdb7MOQ/pdb
EM Map EMD-23926: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Tetrahymena thermophila CU428
Mutation(s): No

Deposited: 2021-05-03 Released: 2021-07-14
Deposition Author(s): Kubo, S., Yang, S.K., Ichikawa, M., Bui, K.H.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8BWY

Literature

Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM.

Kubo, S., Yang, S.K., Black, C.S., Dai, D., Valente-Paterno, M., Gaertig, J., Ichikawa, M., Bui, K.H.

(2021) EMBO Rep 22: e52911-e52911

PubMed: 34338432 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.15252/embr.202152911
Primary Citation of Related Structures:
7MOQ

PubMed Abstract:
Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs' conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryo-electron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with coarse-grained molecular dynamic simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.

Organizational Affiliation

Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.

Macromolecule Content

Total Structure Weight: 2,783.9 kDa
Atom Count: 129,847
Modelled Residue Count: 16,327
Deposited Residue Count: 24,325
Unique protein chains: 22

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative	A	4,168	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for I7M6H4 (Tetrahymena thermophila (strain SB210)) Explore I7M6H4 Go to UniProtKB: I7M6H4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7M6H4
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer arm dynein beta heavy chain	B	4,594	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for I7M9J2 (Tetrahymena thermophila (strain SB210)) Explore I7M9J2 Go to UniProtKB: I7M9J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7M9J2
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein heavy chain, outer arm protein	C	4,620	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q22A67 (Tetrahymena thermophila (strain SB210)) Explore Q22A67 Go to UniProtKB: Q22A67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q22A67
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein intermediate chain 2	AA [auth d], D	667	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for I7M008 (Tetrahymena thermophila (strain SB210)) Explore I7M008 Go to UniProtKB: I7M008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7M008
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar outer dynein arm intermediate protein, putative	BA [auth e], E	670	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q23FU1 (Tetrahymena thermophila (strain SB210)) Explore Q23FU1 Go to UniProtKB: Q23FU1
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q23FU1
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain roadblock-type 2 protein	F	133	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for I7MHB1 (Tetrahymena thermophila (strain SB210)) Explore I7MHB1 Go to UniProtKB: I7MHB1
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7MHB1
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain roadblock-type 2 protein	G	159	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q22MV2 (Tetrahymena thermophila (strain SB210)) Explore Q22MV2 Go to UniProtKB: Q22MV2
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UniProt Group	Q22MV2
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain	H	92	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q1HFW2 (Tetrahymena thermophila) Explore Q1HFW2 Go to UniProtKB: Q1HFW2
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UniProt Group	Q1HFW2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain	I	110	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q1HFX0 (Tetrahymena thermophila) Explore Q1HFX0 Go to UniProtKB: Q1HFX0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1HFX0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain	J	93	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q1HFV9 (Tetrahymena thermophila) Explore Q1HFV9 Go to UniProtKB: Q1HFV9
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1HFV9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain	K	111	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q22R86 (Tetrahymena thermophila (strain SB210)) Explore Q22R86 Go to UniProtKB: Q22R86
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q22R86
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain	L	111	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for W7XJB1 (Tetrahymena thermophila (strain SB210)) Explore W7XJB1 Go to UniProtKB: W7XJB1
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W7XJB1
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain	M	87	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q1HFW0 (Tetrahymena thermophila) Explore Q1HFW0 Go to UniProtKB: Q1HFW0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1HFW0
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain 2A	N	132	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q1HGH8 (Tetrahymena thermophila) Explore Q1HGH8 Go to UniProtKB: Q1HGH8
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UniProt Group	Q1HGH8
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain tctex-type 1 protein	O	117	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for A4VEB3 (Tetrahymena thermophila (strain SB210)) Explore A4VEB3 Go to UniProtKB: A4VEB3
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UniProt Group	A4VEB3
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	P	110	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q1HFX5 (Tetrahymena thermophila) Explore Q1HFX5 Go to UniProtKB: Q1HFX5
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UniProt Group	Q1HFX5
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	DA [auth u] FA [auth q] HA [auth y] Q U DA [auth u], FA [auth q], HA [auth y], Q, U, Y	443	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for P41352 (Tetrahymena thermophila) Explore P41352 Go to UniProtKB: P41352
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41352
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	CA [auth s] EA [auth r] GA [auth w] R S CA [auth s], EA [auth r], GA [auth w], R, S, W	449	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for P41351 (Tetrahymena thermophila) Explore P41351 Go to UniProtKB: P41351
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41351
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer dynein arm docking complex protein oda protein	T	309	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for I7M2C6 (Tetrahymena thermophila (strain SB210)) Explore I7M2C6 Go to UniProtKB: I7M2C6
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7M2C6
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Docking complex 1/2 protein	IA [auth x], V	130	Tetrahymena thermophila CU428	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Docking complex 1 protein	X	555	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q22T00 (Tetrahymena thermophila (strain SB210)) Explore Q22T00 Go to UniProtKB: Q22T00
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UniProt Group	Q22T00
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer dynein arm docking complex protein oda protein	Z	538	Tetrahymena thermophila CU428	Mutation(s): 0
UniProt
Find proteins for Q233H6 (Tetrahymena thermophila (strain SB210)) Explore Q233H6 Go to UniProtKB: Q233H6
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q233H6
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Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain BB [auth w] SDF format, chain NA [auth R] SDF format, chain PA [auth S] SDF format, chain SA [auth W] SDF format, chain VA [auth s] SDF format, chain YA [auth r] MOL2 format, chain BB [auth w] MOL2 format, chain NA [auth R] MOL2 format, chain PA [auth S] MOL2 format, chain SA [auth W] MOL2 format, chain VA [auth s] MOL2 format, chain YA [auth r]	BB [auth w] NA [auth R] PA [auth S] SA [auth W] VA [auth s] BB [auth w], NA [auth R], PA [auth S], SA [auth W], VA [auth s], YA [auth r]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain BB [auth w] Focus chain NA [auth R] Focus chain PA [auth S] Focus chain SA [auth W] Focus chain VA [auth s] Focus chain YA [auth r] Interactions & Density Focus chain BB [auth w] Focus chain NA [auth R] Focus chain PA [auth S] Focus chain SA [auth W] Focus chain VA [auth s] Focus chain YA [auth r]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain KA [auth C] MOL2 format, chain KA [auth C]	KA [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain KA [auth C] Interactions & Density Focus chain KA [auth C]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain AB [auth q] SDF format, chain DB [auth y] SDF format, chain MA [auth Q] SDF format, chain RA [auth U] SDF format, chain UA [auth Y] SDF format, chain XA [auth u] MOL2 format, chain AB [auth q] MOL2 format, chain DB [auth y] MOL2 format, chain MA [auth Q] MOL2 format, chain RA [auth U] MOL2 format, chain UA [auth Y] MOL2 format, chain XA [auth u]	AB [auth q] DB [auth y] MA [auth Q] RA [auth U] UA [auth Y] AB [auth q], DB [auth y], MA [auth Q], RA [auth U], UA [auth Y], XA [auth u]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain AB [auth q] Focus chain DB [auth y] Focus chain MA [auth Q] Focus chain RA [auth U] Focus chain UA [auth Y] Focus chain XA [auth u] Interactions & Density Focus chain AB [auth q] Focus chain DB [auth y] Focus chain MA [auth Q] Focus chain RA [auth U] Focus chain UA [auth Y] Focus chain XA [auth u]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain LA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain LA [auth C]	JA [auth C], LA [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain JA [auth C] Focus chain LA [auth C] Interactions & Density Focus chain JA [auth C] Focus chain LA [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CB [auth w] SDF format, chain OA [auth R] SDF format, chain QA [auth S] SDF format, chain TA [auth W] SDF format, chain WA [auth s] SDF format, chain ZA [auth r] MOL2 format, chain CB [auth w] MOL2 format, chain OA [auth R] MOL2 format, chain QA [auth S] MOL2 format, chain TA [auth W] MOL2 format, chain WA [auth s] MOL2 format, chain ZA [auth r]	CB [auth w] OA [auth R] QA [auth S] TA [auth W] WA [auth s] CB [auth w], OA [auth R], QA [auth S], TA [auth W], WA [auth s], ZA [auth r]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth w] Focus chain OA [auth R] Focus chain QA [auth S] Focus chain TA [auth W] Focus chain WA [auth s] Focus chain ZA [auth r] Interactions & Density Focus chain CB [auth w] Focus chain OA [auth R] Focus chain QA [auth S] Focus chain TA [auth W] Focus chain WA [auth s] Focus chain ZA [auth r]