3WVF | pdb_00003wvf

Crystal structure of YidC from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb3WVF/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli UTI89
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2014-05-20 Released: 2014-12-17 
• Deposition Author(s): Kumazaki, K., Tsukazaki, T., Kishimoto, T., Ishitani, R., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase

Kumazaki, K., Kishimoto, T., Furukawa, A., Mori, H., Tanaka, Y., Dohmae, N., Ishitani, R., Tsukazaki, T., Nureki, O.

(2014) Sci Rep 4: 7299-7299

• PubMed: 25466392 
• DOI: https://doi.org/10.1038/srep07299
• Primary Citation Related Structures: 
  3WVF


• PubMed Abstract: 
  

  Bacterial YidC, an evolutionally conserved membrane protein, functions as a membrane protein chaperone in cooperation with the Sec translocon and as an independent insertase for membrane proteins. In Gram-negative bacteria, the transmembrane and periplasmic regions of YidC interact with the Sec proteins, forming a multi-protein complex for Sec-dependent membrane protein integration. Here, we report the crystal structure of full-length Escherichia coli YidC. The structure reveals that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature of YidC, as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase, and provided structural insight into the multi-protein complex.

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Organizational Affiliation: 
• 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.
Institute for Virus Research, Kyoto University, Shogoin Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
1] Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan [2] JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.75 kDa 
• Atom Count: 6,943 
• Modeled Residue Count: 893 
• Deposited Residue Count: 1,102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein insertase YidC	A, B	551	Escherichia coli UTI89	Mutation(s): 0  Gene Names: yidC Membrane Entity: Yes
UniProt
Find proteins for Q1R4M9 (Escherichia coli (strain UTI89 / UPEC)) Explore Q1R4M9  Go to UniProtKB:  Q1R4M9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.729	α = 78.08
b = 76.011	β = 82.45
c = 91.318	γ = 77.55

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Kumazaki, K., Tsukazaki, T., Kishimoto, T., Ishitani, R., Nureki, O.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description