4UTQ

A structural model of the active ribosome-bound membrane protein insertase YidC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Structural Model of the Active Ribosome-Bound Membrane Protein Insertase Yidc.

Wickles, S.Singharoy, A.Andreani, J.Seemayer, S.Bischoff, L.Berninghausen, O.Soeding, J.Schulten, K.Van Der Sluis, E.O.Beckmann, R.

(2014) Elife 3: 3035

  • DOI: 10.7554/eLife.03035
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the Se ...

    The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.


    Organizational Affiliation

    Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany beckmann@lmb.uni-muenchen.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MEMBRANE PROTEIN INSERTASE YIDCA548Escherichia coliMutation(s): 0 
Find proteins for P25714 (Escherichia coli (strain K12))
Explore P25714 
Go to UniProtKB:  P25714
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT CZ79Escherichia coliMutation(s): 0 
Find proteins for P68699 (Escherichia coli (strain K12))
Explore P68699 
Go to UniProtKB:  P68699
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection