5MG3

EM fitted model of bacterial holo-translocon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.

Botte, M.Zaccai, N.R.Nijeholt, J.L.Martin, R.Knoops, K.Papai, G.Zou, J.Deniaud, A.Karuppasamy, M.Jiang, Q.Roy, A.S.Schulten, K.Schultz, P.Rappsilber, J.Zaccai, G.Berger, I.Collinson, I.Schaffitzel, C.

(2016) Sci Rep 6: 38399-38399

  • DOI: 10.1038/srep38399

  • PubMed Abstract: 
  • The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining ...

    The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon. Their arrangement around a central lipid-containing pool conveys an unexpected, but compelling mechanism for membrane-protein insertion. The periplasmic domains of YidC and SecD are poised at the protein-channel exit-site of SecY, presumably to aid the emergence of translocating polypeptides. The SecY lateral gate for membrane-insertion is adjacent to the membrane 'insertase' YidC. Absolute-scale SANS employing a novel contrast-match-point analysis revealed a dynamic complex adopting open and compact configurations around an adaptable central lipid-filled chamber, wherein polytopic membrane-proteins could fold, sheltered from aggregation and proteolysis.


    Organizational Affiliation

    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom.,Department of Physics, University of Illinois Urbana Champaign, 3217 Beckman Institute, 405 N Mathews Ave., Urbana, IL 61801, USA.,Institut Laue Langevin, 71 Avenue des Martyrs, F-38042 Grenoble, France.,Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), U964 INSERM, UMR7104 CNRS; University of Strasbourg, 1 Rue Laurent Fries, BP10142, 67404 Illkirch, France.,School of Biochemistry, University of Bristol, BS8 1TD, United Kingdom.,CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.,European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France.,Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecY
Y
458Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secY (prlA)
Find proteins for P0AGA2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGA2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecE
E
140Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secE (prlG)
Find proteins for P0AG96 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG96
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein-export membrane protein SecG
G
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secG
Find proteins for P0AG99 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG99
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecD
D
622Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secD
Find proteins for P0AG90 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG90
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecF
F
323Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secF
Find proteins for P0AG93 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG93
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Membrane protein insertase YidC
C
559Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yidC
Find proteins for P25714 (Escherichia coli (strain K12))
Go to UniProtKB:  P25714
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Baden-Wurttemberg StiftungGermanyMeth-P-LS-4
French National Research AgencyFranceANR- 09-JCJC-0044
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P000940/1

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Data collection