9RSJ | pdb_00009rsj

Cryo-EM structure of MATE transporter NorM-VC in complex with doxorubicin

• PDB DOI: https://doi.org/10.2210/pdb9RSJ/pdb
• EM Map EMD-54220: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Vibrio cholerae, synthetic construct, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-07-01 Released: 2025-11-26 
• Deposition Author(s): Romane, K., Hsieh, P.Y., Kowal, J., Locher, K.P., van Veen, H.W.
• Funding Organization(s): Swiss National Science Foundation, Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Doxorubicin Recognition and Transport by the MATE Multidrug Transporter NorM From Vibrio cholerae.

Hsieh, P.Y., Romane, K., Kowal, J., Locher, K.P., van Veen, H.W.

(2025) J Mol Biology 438: 169549-169549

• PubMed: 41260293 
• DOI: https://doi.org/10.1016/j.jmb.2025.169549
• Primary Citation of Related Structures:  
  9RSJ


• PubMed Abstract: 
  

  Multidrug and toxic compound extrusion (MATE) transport proteins contribute to multidrug resistance in human pathogens by extruding various cytotoxic compounds from the cellular interior. Despite their importance across all domains of life, the specificities and mechanisms of substrate transport of these proteins remain poorly understood due to limited structural and functional information. Here, we determined the cryo-electron microscopy structure of NorM from Vibrio cholerae (NorM-VC) in complex with the anthracycline antibiotic doxorubicin, using the NabFab approach. The structure reveals that the doxorubicin-binding pocket is located halfway through the membrane, within the C-lobe of the protein. Functional studies targeting the doxorubicin-interacting residues validated the binding pocket and enabled detailed analysis of the doxorubicin transport reaction. Our findings indicate doxorubicin binding within a multisite binding chamber engaged in a general transport mechanism for a variety of substrates.

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Organizational Affiliation: 
• Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.
Institute of Molecular Biology and Biophysics, ETH Zürich 8093 Zürich, Switzerland.
Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 127.13 kDa 
• Atom Count: 8,664 
• Modeled Residue Count: 1,134 
• Deposited Residue Count: 1,170 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug resistance protein NorM	A	461	Vibrio cholerae	Mutation(s): 0  Gene Names: VCM66_1481
UniProt
Find proteins for C3LML9 (Vibrio cholerae serotype O1 (strain M66-2)) Explore C3LML9  Go to UniProtKB:  C3LML9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NabFab HC	B [auth H]	239	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NabFab LC	C [auth L]	215	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NorM-Nb17_4	D [auth N]	132	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-Fab nanobody	E [auth K]	123	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DM2 (Subject of Investigation/LOI)	F [auth A]	DOXORUBICIN C27 H29 N O11 AOJJSUZBOXZQNB-TZSSRYMLSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Romane, K., Hsieh, P.Y., Kowal, J., Locher, K.P., van Veen, H.W.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_214834
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/K017713/1

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Data collection, Database references