8K1M

mycobacterial efflux pump, apo state

• PDB DOI: https://doi.org/10.2210/pdb8K1M/pdb
• EM Map EMD-36795: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-07-11 Released: 2024-07-17 
• Deposition Author(s): Wang, Y., Wu, F., Zhang, L., Rao, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

mycobacterial efflux pump, apo state

Wang, Y., Wu, F., Zhang, L., Rao, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 121.36 kDa 
• Atom Count: 7,148 
• Modelled Residue Count: 951 
• Deposited Residue Count: 1,126 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux system permease protein Rv1217c	A [auth B]	548	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv1217c Membrane Entity: Yes
UniProt
Find proteins for O05318 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O05318  Go to UniProtKB:  O05318

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux system ATP-binding protein Rv1218c	B [auth C], C [auth D]	289	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv1218c EC: 7.6.2 Membrane Entity: Yes
UniProt
Find proteins for O86311 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O86311  Go to UniProtKB:  O86311

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	E [auth B]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
L9Q (Subject of Investigation/LOI)	D [auth B]	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C41 H80 N O8 P JQKOHRZNEOQNJE-VYCVAHKRSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Wang, Y., Wu, F., Zhang, L., Rao, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32170703

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release