3WVF

Crystal structure of YidC from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1038/srep07299

  • 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 peri ...

    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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane protein insertase YidC
A, B
551Escherichia coli (strain UTI89 / UPEC)Mutation(s): 0 
Gene Names: yidC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec and Translocase Proteins
Protein: 
YidC insertase, full length
Find proteins for Q1R4M9 (Escherichia coli (strain UTI89 / UPEC))
Go to UniProtKB:  Q1R4M9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.729α = 78.08
b = 76.011β = 82.45
c = 91.318γ = 77.55
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release