9V52 | pdb_00009v52

Structure of TolC and YbjP closed state complex

PDB DOI: https://doi.org/10.2210/pdb9V52/pdb
EM Map EMD-64784: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-25 Released: 2025-11-05
Deposition Author(s): Ge, X.F., Gu, Z.W., Wang, J.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9V52

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

Literature

Structural mechanisms of pump assembly and drug transport in the AcrAB-TolC efflux system

Ge, X., Gu, Z., Wang, J.

(2025) Elife

DOI: https://doi.org/10.7554/elife.109684.1

Macromolecule Content

Total Structure Weight: 218.39 kDa
Atom Count: 13,539
Modeled Residue Count: 1,752
Deposited Residue Count: 1,992
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein TolC	A [auth C1], C [auth C3], E [auth C2]	493	Escherichia coli K-12	Mutation(s): 0 Gene Names: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
UniProt
Find proteins for P02930 (Escherichia coli (strain K12)) Explore P02930 Go to UniProtKB: P02930
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02930
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein YbjP	B [auth P1], D [auth P3], F [auth P2]	171	Escherichia coli K-12	Mutation(s): 0 Gene Names: ybjP, b0865, JW0849
UniProt
Find proteins for P75818 (Escherichia coli (strain K12)) Explore P75818 Go to UniProtKB: P75818
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75818
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371254
National Natural Science Foundation of China (NSFC)	China	32171190

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release
Version 1.1: 2025-11-12
Changes: Data collection, Database references
Version 1.2: 2025-12-31
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.