9GI2 | pdb_00009gi2

Truncated MmpL4 in nanodiscs in absence of substrate

• PDB DOI: https://doi.org/10.2210/pdb9GI2/pdb
• EM Map EMD-51368: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli MC1061, Mycobacterium tuberculosis
• Expression System: Escherichia coli MC1061
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2024-08-16 Released: 2025-02-19 
• Deposition Author(s): Earp, J.C., Garaeva, A.A., Seeger, M.A.
• Funding Organization(s): European Research Council (ERC), University of Zurich, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural basis of siderophore export and drug efflux by Mycobacterium tuberculosis.

Earp, J.C., Garaeva, A.A., Meikle, V., Niederweis, M., Seeger, M.A.

(2025) Nat Commun 16: 1934-1934

• PubMed: 39994240 
• DOI: https://doi.org/10.1038/s41467-025-56888-6
• Primary Citation Related Structures: 
  9GI0, 9GI2, 9GI3


• PubMed Abstract: 
  

  To replicate and cause disease, Mycobacterium tuberculosis secretes siderophores called mycobactins to scavenge iron from the human host. Two closely related transporters, MmpL4 and MmpL5, are required for mycobactin secretion and drug efflux. In clinical strains, overproduction of MmpL5 confers resistance towards bedaquiline and clofazimine, key drugs to combat multidrug resistant tuberculosis. Here, we present cryogenic-electron microscopy structures of MmpL4 and identify a mycobactin binding site, which is accessible from the cytosol and also required for bedaquiline efflux. An unusual coiled-coil domain predicted to extend 130 Å into the periplasm is essential for mycobactin and bedaquiline efflux by MmpL4 and MmpL5. The mycobacterial acyl carrier protein MbtL forms a complex with MmpL4, indicating that mycobactin synthesis and export are coupled. Thus, MmpL4 and MmpL5 constitute the core components of a unique multi-subunit machinery required for iron acquisition and drug efflux by M. tuberculosis.

---

Organizational Affiliation: 
• Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA. [e-mail].
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland. [e-mail].
National Center for Mycobacteria, University of Zurich, Zurich, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 92.45 kDa 
• Atom Count: 6,024 
• Modeled Residue Count: 796 
• Deposited Residue Count: 861 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	A	78	Escherichia coli MC1061	Mutation(s): 0
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8  Go to UniProtKB:  P0A6A8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Siderophore exporter MmpL4	B	783	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: mmpL4, MT0466 Membrane Entity: Yes
UniProt
Find proteins for P9WJV3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJV3  Go to UniProtKB:  P9WJV3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.2
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Earp, J.C., Garaeva, A.A., Seeger, M.A.

---

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	772190
University of Zurich	Switzerland	FK-21-041
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21 AI151239
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI137338

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release
  
• Version 1.1: 2025-03-05
  Changes: Data collection, Database references