9J3E | pdb_00009j3e

Cryo-EM structure of TMexCD1-TOprJ1 in complex with 1-(1-naphthylmethyl)piperazine

• PDB DOI: https://doi.org/10.2210/pdb9J3E/pdb
• EM Map EMD-61115: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-08 Released: 2025-08-13 
• Deposition Author(s): Shi, Y., Feng, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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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 of TMexCD1-TOprJ1

Shi, Y., Feng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B3C3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 750.81 kDa 
• Atom Count: 47,916 
• Modeled Residue Count: 6,330 
• Deposited Residue Count: 6,951 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RND efflux system, OprJ-like protein	A, B, C	483	Klebsiella pneumoniae	Mutation(s): 0
UniProt
Find proteins for A0A411AKN6 (Klebsiella pneumoniae) Explore A0A411AKN6  Go to UniProtKB:  A0A411AKN6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RND efflux system, MexC-like protein	D, E, F, G, H, I	395	Klebsiella pneumoniae	Mutation(s): 0
UniProt
Find proteins for A0A411AKL2 (Klebsiella pneumoniae) Explore A0A411AKL2  Go to UniProtKB:  A0A411AKL2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Efflux pump membrane transporter	J [auth K], K [auth J], L	1,044	Klebsiella pneumoniae	Mutation(s): 0
UniProt
Find proteins for A0A411AKL6 (Klebsiella pneumoniae) Explore A0A411AKL6  Go to UniProtKB:  A0A411AKL6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EAN (Subject of Investigation/LOI)	M [auth K], N [auth J], O [auth L]	1-(naphthalen-1-ylmethyl)piperazine C15 H18 N2 HGYDREHWXXUUIS-UHFFFAOYSA-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	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Shi, Y., Feng, Y.

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

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release