3WO7

Crystal structure of YidC from Bacillus halodurans (form II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of Sec-independent membrane protein insertion by YidC.

Kumazaki, K.Chiba, S.Takemoto, M.Furukawa, A.Nishiyama, K.Sugano, Y.Mori, T.Dohmae, N.Hirata, K.Nakada-Nakura, Y.Maturana, A.D.Tanaka, Y.Mori, H.Sugita, Y.Arisaka, F.Ito, K.Ishitani, R.Tsukazaki, T.Nureki, O.

(2014) Nature 509: 516-520

  • DOI: 10.1038/nature13167
  • Primary Citation of Related Structures:  
    3WO6, 3WO7

  • PubMed Abstract: 
  • Newly synthesized membrane proteins must be accurately inserted into the membrane, folded and assembled for proper functioning. The protein YidC inserts its substrates into the membrane, thereby facilitating membrane protein assembly in bacteria; the ...

    Newly synthesized membrane proteins must be accurately inserted into the membrane, folded and assembled for proper functioning. The protein YidC inserts its substrates into the membrane, thereby facilitating membrane protein assembly in bacteria; the homologous proteins Oxa1 and Alb3 have the same function in mitochondria and chloroplasts, respectively. In the bacterial cytoplasmic membrane, YidC functions as an independent insertase and a membrane chaperone in cooperation with the translocon SecYEG. Here we present the crystal structure of YidC from Bacillus halodurans, at 2.4 Å resolution. The structure reveals a novel fold, in which five conserved transmembrane helices form a positively charged hydrophilic groove that is open towards both the lipid bilayer and the cytoplasm but closed on the extracellular side. Structure-based in vivo analyses reveal that a conserved arginine residue in the groove is important for the insertion of membrane proteins by YidC. We propose an insertion mechanism for single-spanning membrane proteins, in which the hydrophilic environment generated by the groove recruits the extracellular regions of substrates into the low-dielectric environment of the membrane.


    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane protein insertase YidC 2AB254Bacillus halodurans C-125Mutation(s): 1 
Gene Names: yidC2BH1169
Find proteins for Q9KDP2 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KDP2 
Go to UniProtKB:  Q9KDP2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.033α = 90
b = 70.058β = 92.05
c = 82.91γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
BSSdata collection
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Structure summary
  • Version 1.2: 2019-12-18
    Changes: Database references