9IQE | pdb_00009iqe

Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ADP-bound IFasym-3 (peptidisc) state (ATP 37degrees C treated)

• PDB DOI: https://doi.org/10.2210/pdb9IQE/pdb
• EM Map EMD-60789: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-07-12 Released: 2025-05-14 
• Deposition Author(s): Lan, Y., Li, J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and mechanism of a mycobacterial isoniazid efflux pump MsRv1273c/72c with a degenerate nucleotide-binding site.

Yu, J., Lan, Y., Zhu, C., Chen, Z., Pan, J., Shi, Y., Yang, L., Hu, T., Gao, Y., Zhao, Y., Chen, X., Yang, X., Lu, S., Guddat, L.W., Yang, H., Rao, Z., Li, J.

(2025) Nat Commun 16: 3969-3969

• PubMed: 40295516 
• DOI: https://doi.org/10.1038/s41467-025-59300-5
• Primary Citation Related Structures: 
  8WCW, 8WCX, 8XSR, 8XSS, 8XST, 9IQE, 9IQF, 9IQG, 9KWI


• PubMed Abstract: 
  

  Heterodimeric ATP-binding cassette (ABC) transporters containing one catalytically impaired degenerate nucleotide-binding site (NBS) have a mechanism different from those with two active NBSs. However, the structural basis of their transport mechanism remains to be explained. Here, we determine mycobacterial MsRv1273c/72c to be an isoniazid efflux pump and determine several structures by cryo-electron microscopy showing specific asymmetrical features including an N-terminal extending loop and a periplasmic helical hairpin only found in MsRv1272c. In addition, we capture three distinct asymmetric states where the nucleotide-binding domains are partially dimerized at the degenerate site. Using these intermediate states, the D-WalkerB loop and X-signature loop of MsRv1272c modulate and couple the function of both NBSs through conformational changes. Thus, these data provide insights into the mechanism of this heterodimeric ABC transporter containing a degenerate NBS. The structures also provide a framework for the rational design of anti-tuberculosis drugs targeting this drug-efflux pump.

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Organizational Affiliation: 
• Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300353, China. [e-mail].
Laboratory of Structural Biology, Tsinghua University, 100084, Beijing, China. [e-mail].
Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, 510005, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 134.36 kDa 
• Atom Count: 9,118 
• Modeled Residue Count: 1,193 
• Deposited Residue Count: 1,233 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, ATP-binding protein	A	590	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_5008 EC: 7.6.2 Membrane Entity: Yes
UniProt
Find proteins for P9WQJ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQJ1  Go to UniProtKB:  P9WQJ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter transmembrane region	B	643	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEI_4882, MSMEG_5009 EC: 7.6.2 Membrane Entity: Yes
UniProt
Find proteins for P9WQJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQJ3  Go to UniProtKB:  P9WQJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	C [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Lan, Y., Li, J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA1300900
Ministry of Science and Technology (MoST, China)	China	2022YFC230900
Other government		22ZR1441600

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release