7NVH | pdb_00007nvh

Cryo-EM structure of the mycolic acid transporter MmpL3 from M. tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb7NVH/pdb
• EM Map EMD-12604: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2021-03-15 Released: 2021-06-16 
• Deposition Author(s): Adams, O., Deme, J.C., Parker, J.L., Lea, S.M., Newstead, S.
• Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target.

Adams, O., Deme, J.C., Parker, J.L., Fowler, P.W., Lea, S.M., Newstead, S.

(2021) Structure 29: 1182-1191.e4

• PubMed: 34242558 
• DOI: https://doi.org/10.1016/j.str.2021.06.013
• Primary Citation Related Structures: 
  7NVH


• PubMed Abstract: 
  

  Tuberculosis (TB) is the leading cause of death from a single infectious agent and in 2019 an estimated 10 million people worldwide contracted the disease. Although treatments for TB exist, continual emergence of drug-resistant variants necessitates urgent development of novel antituberculars. An important new target is the lipid transporter MmpL3, which is required for construction of the unique cell envelope that shields Mycobacterium tuberculosis (Mtb) from the immune system. However, a structural understanding of the mutations in Mtb MmpL3 that confer resistance to the many preclinical leads is lacking, hampering efforts to circumvent resistance mechanisms. Here, we present the cryoelectron microscopy structure of Mtb MmpL3 and use it to comprehensively analyze the mutational landscape of drug resistance. Our data provide a rational explanation for resistance variants local to the central drug binding site, and also highlight a potential alternative route to resistance operating within the periplasmic domain.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford OX1 3RE, UK; Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK; National Institute of Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe, Oxford OX3 9DU, UK.
The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford OX1 3RE, UK; Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA. Electronic address: [e-mail].
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.53 kDa 
• Atom Count: 5,528 
• Modeled Residue Count: 717 
• Deposited Residue Count: 761 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trehalose monomycolate exporter MmpL3	A	761	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: mmpL3, Rv0206c, MTCY08D5.01c, MTV033.14c Membrane Entity: Yes
UniProt
Find proteins for P9WJV5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJV5  Go to UniProtKB:  P9WJV5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AV0	B [auth A]	Lauryl Maltose Neopentyl Glycol C47 H88 O22 MADJBYLAYPCCOO-VWHTXWAPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Adams, O., Deme, J.C., Parker, J.L., Lea, S.M., Newstead, S.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	201536
Wellcome Trust	United Kingdom	215519
Wellcome Trust	United Kingdom	219531
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/S021043/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	S021264
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M011224/1

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2021-07-21
  Changes: Database references
• Version 1.2: 2021-10-20
  Changes: Data collection, Database references
• Version 1.3: 2022-12-21
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2024-07-10
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2025-07-09
  Changes: Data collection, Structure summary