9QPT | pdb_00009qpt

Single particle cryo-EM structure of MdtF V610F with bound Rhodamine 6G


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QPT

This is version 1.1 of the entry. See complete history

Literature

Molecular basis for multidrug efflux by an anaerobic-associated RND transporter.

Lawrence, R.Athar, M.Uddin, M.R.Adams, C.Sousa, J.S.Durrant, O.Lellman, S.Sutton, L.Keevil, C.W.Patel, N.Prosser, C.E.McMillan, D.Zgurskaya, H.I.Vargiu, A.V.Ahdash, Z.Reading, E.

(2025) Nat Commun 16: 10601-10601

  • DOI: https://doi.org/10.1038/s41467-025-65565-7
  • Primary Citation Related Structures: 
    9QPR, 9QPS, 9QPT

  • PubMed Abstract: 

    Bacteria can resist antibiotics and toxic substances within demanding ecological settings, such as low oxygen, extreme acid, and during nutrient starvation. MdtEF, a proton motive force-driven efflux pump from the resistance-nodulation-cell division (RND) superfamily, is upregulated in these conditions but its molecular mechanism is unknown. Here, we report cryo-electron microscopy structures of Escherichia coli multidrug transporter MdtF within native-lipid nanodiscs, including a single-point mutant with an altered multidrug phenotype and associated substrate-bound form. Drug binding domain and channel conformational plasticity likely governs substrate polyspecificity, analogous to closely related, constitutively expressed counterpart, AcrB. Whereas we discover distinct transmembrane state transitions within MdtF, which create a more engaged proton relay network, altered drug transport allostery and an acid-responsive increase in efflux efficiency. Our findings provide mechanistic insights necessary to understand bacterial xenobiotic and toxin removal by MdtF and its role within nutrient-depleted and acid stress settings, as endured in the gastrointestinal tract.


  • Organizational Affiliation
    • School of Biological Sciences, University of Southampton, Southampton, UK.

Macromolecule Content 

  • Total Structure Weight: 360.79 kDa 
  • Atom Count: 24,061 
  • Modeled Residue Count: 3,054 
  • Deposited Residue Count: 3,165 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multidrug resistance protein MdtF
A, B, C
1,055Escherichia coli K-12Mutation(s): 1 
Gene Names: mdtFyhiVb3514JW3482
UniProt
Find proteins for P37637 (Escherichia coli (strain K12))
Explore P37637 
Go to UniProtKB:  P37637
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37637
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY

Query on PTY



Download:Ideal Coordinates CCD File
E [auth A]
EA [auth C]
F [auth A]
FA [auth C]
G [auth A]
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
LA [auth C],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
RHQ
(Subject of Investigation/LOI)

Query on RHQ



Download:Ideal Coordinates CCD File
DA [auth C]RHODAMINE 6G
C28 H31 N2 O3
IWWWBRIIGAXLCJ-KRUMMXJUSA-O
D12

Query on D12



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
KA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
KA [auth C],
M [auth A],
MA [auth C],
N [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T008709/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Data collection, Database references