8ZAR | pdb_00008zar

EmrAB-TolC MFS-type tripartite multidrug efflux pump FA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

A model for drug transport across two membranes of Gram-negative bacteria by an MFS tripartite assembly.

Zhong, Z.Maimaiti, T.Jackson, M.L.Dong, R.Gao, X.Ouyang, Q.Wang, W.Guo, J.Li, S.Shang, W.Liu, H.Jiang, H.Zhang, S.Zachariae, U.Luisi, B.F.Chao, Y.Du, D.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-70500-5
  • Primary Citation Related Structures: 
    8ZAL, 8ZAR

  • PubMed Abstract: 

    Transport of proteins and small molecules across cellular membrane is crucial for bacterial interaction with the environment and survival against antibiotics. In Gram-negative bacteria that possess two layers of membranes, specialized macromolecular machines are required to transport substrates across the cell envelope, often via an indirect stepwise process. The major facilitator superfamily (MFS)-type tripartite efflux pumps use proton electrochemical gradient to extrude drugs in diverse bacterial species, but the architecture of the assembly and structural mechanisms remain elusive. A representative MFS-type tripartite efflux pump, EmrAB-TolC, mediates resistance to multiple antimicrobial drugs through proton-coupled EmrB, a member of the DHA2 transporter family. Here, we report the high-resolution (3.13 Å) structure of the EmrAB-TolC pump, revealing a distinct, asymmetric architecture emerging from the assembly of TolC:EmrA:EmrB with a ratio of 3:6:1 and contacts that are essential for the pump assembly. Key residues involved in drug transport are identified and corroborated by mutagenesis and antibiotic sensitivity assays. The structural and functional data support a model for one-step drug transport by the MFS pump across the entire envelope of Gram-negative bacteria.


  • Organizational Affiliation
    • School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 495.59 kDa 
  • Atom Count: 29,869 
  • Modeled Residue Count: 3,880 
  • Deposited Residue Count: 4,523 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multidrug export protein EmrA
A, B, C, D, E
A, B, C, D, E, F
401Escherichia coli K-12Mutation(s): 0 
Gene Names: emrA
UniProt
Find proteins for P27303 (Escherichia coli (strain K12))
Explore P27303 
Go to UniProtKB:  P27303
Entity Groups
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UniProt GroupP27303
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Multidrug export protein EmrBG [auth J]614Escherichia coli K-12Mutation(s): 0 
Gene Names: emrB
UniProt
Find proteins for P0AEJ0 (Escherichia coli (strain K12))
Explore P0AEJ0 
Go to UniProtKB:  P0AEJ0
Entity Groups
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UniProt GroupP0AEJ0
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein TolCH [auth G],
I [auth H],
J [auth I]
501Escherichia coli K-12Mutation(s): 1 
Gene Names: tolC
UniProt
Find proteins for P02930 (Escherichia coli (strain K12))
Explore P02930 
Go to UniProtKB:  P02930
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02930
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971133

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection
  • Version 1.2: 2026-05-13
    Changes: Data collection, Database references