9V53 | pdb_00009v53

Structure of TolC, YbjP, and AcrABZ complex

• PDB DOI: https://doi.org/10.2210/pdb9V53/pdb
• EM Map EMD-64785: 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 18-mer - A6B3C3D3E3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 828.72 kDa 
• Atom Count: 53,464 
• Modeled Residue Count: 7,037 
• Deposited Residue Count: 7,668 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein TolC	A [auth C1], B [auth C2], C [auth C3]	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein YbjP	D [auth P1], E [auth P2], F [auth P3]	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrA	G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	397	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrA, lir, mtcA, b0463, JW0452
UniProt
Find proteins for P0AE06 (Escherichia coli (strain K12)) Explore P0AE06  Go to UniProtKB:  P0AE06

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	M [auth BL], O [auth BT], Q [auth BO]	1,049	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrB, acrE, b0462, JW0451
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump accessory protein AcrZ	N [auth ZL], P [auth ZT], R [auth ZO]	49	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrZ, ybhT, b0762, JW5102
UniProt
Find proteins for P0AAW9 (Escherichia coli (strain K12)) Explore P0AAW9  Go to UniProtKB:  P0AAW9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Ge, X.F., Gu, Z.W., Wang, J.W.

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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  

• 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