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

    European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France.




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