45LQ | pdb_000045lq

Crystal structure of Escherichia coli YidC in complex with YibN

• PDB DOI: https://doi.org/10.2210/pdb45LQ/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2026-09-02 Released: 2026-10-07 
• Deposition Author(s): Takahashi, Y.S., Miyazaki, R., Kohga, H., Tsukazaki, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.09 Å
• R-Value Free: 
  0.325 (Depositor), 0.325 (DCC) 
• R-Value Work: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Starting Models: experimental, in silico

Literature

Crystal structure of Escherichia coli YidC in complex with YibN

Takahashi, Y.S., Miyazaki, R., Kohga, H., Tsukazaki, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 166.74 kDa 
• Atom Count: 8,392 
• Modeled Residue Count: 1,052 
• Deposited Residue Count: 1,484 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein insertase YidC	A, B [auth D]	548	Escherichia coli	Mutation(s): 0  Gene Names: yidC, b3705, JW3683
UniProt
Find proteins for P25714 (Escherichia coli (strain K12)) Explore P25714  Go to UniProtKB:  P25714

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein insertase YidC	C [auth B], E	27	Escherichia coli	Mutation(s): 0  Gene Names: yidC, b3705, JW3683
UniProt
Find proteins for P25714 (Escherichia coli (strain K12)) Explore P25714  Go to UniProtKB:  P25714

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
YibN	D [auth C], F	167	Escherichia coli	Mutation(s): 0  Gene Names: yibN, b3611, JW3586
UniProt
Find proteins for P0AG27 (Escherichia coli (strain K12)) Explore P0AG27  Go to UniProtKB:  P0AG27

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.09 Å
• R-Value Free:  0.325 (Depositor), 0.325 (DCC) 
• R-Value Work:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.6	α = 90
b = 182.85	β = 91.42
c = 100.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Takahashi, Y.S., Miyazaki, R., Kohga, H., Tsukazaki, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release