8Z5X | pdb_00008z5x

Cryo-EM structure of the MS ring with the proximal rod and the export apparatus (C1) within the polar flagellar motor

PDB DOI: https://doi.org/10.2210/pdb8Z5X/pdb
EM Map EMD-39787: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Vibrio alginolyticus
Mutation(s): No

Deposited: 2024-04-18 Released: 2025-10-22
Deposition Author(s): Zhang, L., Tan, J.X., Zhou, Y., Zhu, Y.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.64 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the MS ring with the proximal rod and the export apparatus (C1) within the polar flagellar motor

Zhang, L., Tan, J.X., Zhou, Y., Zhu, Y.Q.

To be published.

Macromolecule Content

Total Structure Weight: 5,115.99 kDa
Atom Count: 88,315
Modeled Residue Count: 11,398
Deposited Residue Count: 46,459
Unique protein chains: 10

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliP	A [auth 0], AA [auth AP], J [auth 9], VA [auth Ak], WA [auth Al]	289	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A1W6TTE6 (Vibrio alginolyticus) Explore A0A1W6TTE6 Go to UniProtKB: A0A1W6TTE6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1W6TTE6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar M-ring protein	AB [auth E] AC [auth e] B [auth 1] BB [auth F] BC [auth f] AB [auth E], AC [auth e], B [auth 1], BB [auth F], BC [auth f], C [auth 2], CB [auth G], CC [auth g], D [auth 3], DB [auth H], DC [auth h], E [auth 4], EB [auth I], EC [auth i], F [auth 5], FB [auth J], FC [auth j], GB [auth K], GC [auth k], HB [auth L], HC [auth l], IB [auth M], IC [auth m], JB [auth N], JC [auth n], K [auth A], KB [auth O], KC [auth o], L [auth AA], LB [auth P], LC [auth p], M [auth AB], MB [auth Q], MC [auth q], N [auth AC], NB [auth R], NC [auth r], O [auth AD], OB [auth S], OC [auth s], P [auth AE], PB [auth T], PC [auth t], Q [auth AF], QB [auth U], QC [auth u], R [auth AG], RB [auth V], RC [auth v], S [auth AH], SB [auth W], SC [auth w], T [auth AI], TB [auth X], TC [auth x], U [auth AJ], UB [auth Y], UC [auth y], V [auth AK], VB [auth Z], VC [auth z], W [auth AL], WB [auth a], X [auth AM], XA [auth B], XB [auth b], Y [auth AN], YA [auth C], YB [auth c], Z [auth AO], ZA [auth D], ZB [auth d]	580	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for Q75N27 (Vibrio alginolyticus) Explore Q75N27 Go to UniProtKB: Q75N27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q75N27
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliQ	BA [auth AQ], CA [auth AR], G [auth 6], H [auth 7]	89	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0T7EAU9 (Vibrio diabolicus) Explore A0A0T7EAU9 Go to UniProtKB: A0A0T7EAU9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0T7EAU9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FliR	I [auth 8]	260	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0H0YFV7 (Vibrio alginolyticus) Explore A0A0H0YFV7 Go to UniProtKB: A0A0H0YFV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H0YFV7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal body rod protein FlgB	DA [auth AS], EA [auth AT], FA [auth AU], GA [auth AV], HA [auth AW]	131	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9LZG6 (Vibrio alginolyticus) Explore A0A0G9LZG6 Go to UniProtKB: A0A0G9LZG6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0G9LZG6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgC	IA [auth AX] JA [auth AY] KA [auth AZ] LA [auth Aa] MA [auth Ab] IA [auth AX], JA [auth AY], KA [auth AZ], LA [auth Aa], MA [auth Ab], NA [auth Ac]	137	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A0G9LZH2 (Vibrio alginolyticus) Explore A0A0G9LZH2 Go to UniProtKB: A0A0G9LZH2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0G9LZH2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar hook-basal body complex protein FliE	OA [auth Ad] PA [auth Ae] QA [auth Af] RA [auth Ag] SA [auth Ah] OA [auth Ad], PA [auth Ae], QA [auth Af], RA [auth Ag], SA [auth Ah], TA [auth Ai]	103	Vibrio alginolyticus	Mutation(s): 0
UniProt
Find proteins for A0A2L2K9J6 (Vibrio diabolicus) Explore A0A2L2K9J6 Go to UniProtKB: A0A2L2K9J6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2L2K9J6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthetic protein FlhB	UA [auth Aj]	376	Vibrio alginolyticus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine-modelled FlgB-Dc loop	AD [auth Aq], WC [auth Am], XC [auth An], YC [auth Ao], ZC [auth Ap]	13	Vibrio alginolyticus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
FliE-helix 1	BD [auth Ar] CD [auth As] DD [auth At] ED [auth Au] FD [auth Av] BD [auth Ar], CD [auth As], DD [auth At], ED [auth Au], FD [auth Av], GD [auth Aw]	17	Vibrio alginolyticus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.64 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81925024
National Natural Science Foundation of China (NSFC)	China	U23A20163
Ministry of Science and Technology (MoST, China)	China	2017YFA0503900

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 8Z5X | pdb_00008z5x

Cryo-EM structure of the MS ring with the proximal rod and the export apparatus (C1) within the polar flagellar motor

Cryo-EM structure of the MS ring with the proximal rod and the export apparatus (C1) within the polar flagellar motor

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

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Sequence Annotations

Entity ID: 4

UniProt

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Sequence Annotations

Entity ID: 5

UniProt

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Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

Entity Groups

Sequence Annotations

Entity ID: 9

Entity Groups

Sequence Annotations

Entity ID: 10

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

8Z5X | pdb_00008z5x