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 5MG3 | pdb_00005mg3

EM fitted model of bacterial holo-translocon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 5MG3

This is version 2.0 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: https://doi.org/10.1038/srep38399
  • Primary Citation Related Structures: 
    5MG3

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 245.74 kDa 
  • Atom Count: 13,097 
  • Modeled Residue Count: 1,698 
  • Deposited Residue Count: 2,238 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein translocase subunit SecYA [auth Y]458Escherichia coliMutation(s): 0 
Gene Names: secY, prlA, b3300, JW3262
Membrane Entity: Yes 
UniProt
Find proteins for P0AGA2 (Escherichia coli (strain K12))
Explore P0AGA2 
Go to UniProtKB:  P0AGA2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AGA2
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein translocase subunit SecEB [auth E]140Escherichia coliMutation(s): 0 
Gene Names: secE, prlG, b3981, JW3944
Membrane Entity: Yes 
UniProt
Find proteins for P0AG96 (Escherichia coli (strain K12))
Explore P0AG96 
Go to UniProtKB:  P0AG96
Entity Groups
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UniProt GroupP0AG96
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein-export membrane protein SecGC [auth G]136Escherichia coliMutation(s): 0 
Gene Names: secG, b3175, JW3142
Membrane Entity: Yes 
UniProt
Find proteins for P0AG99 (Escherichia coli (strain K12))
Explore P0AG99 
Go to UniProtKB:  P0AG99
Entity Groups
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UniProt GroupP0AG99
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein translocase subunit SecD622Escherichia coliMutation(s): 0 
Gene Names: secD, b0408, JW0398
Membrane Entity: Yes 
UniProt
Find proteins for P0AG90 (Escherichia coli (strain K12))
Explore P0AG90 
Go to UniProtKB:  P0AG90
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UniProt GroupP0AG90
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein translocase subunit SecFE [auth F]323Escherichia coliMutation(s): 0 
Gene Names: secF, b0409, JW0399
Membrane Entity: Yes 
UniProt
Find proteins for P0AG93 (Escherichia coli (strain K12))
Explore P0AG93 
Go to UniProtKB:  P0AG93
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UniProt GroupP0AG93
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane protein insertase YidCF [auth C]559Escherichia coliMutation(s): 0 
Gene Names: yidC, b3705, JW3683
Membrane Entity: Yes 
UniProt
Find proteins for P25714 (Escherichia coli (strain K12))
Explore P25714 
Go to UniProtKB:  P25714
Entity Groups
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UniProt GroupP25714
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references
  • Version 2.0: 2024-11-20
    Changes: Advisory, Atomic model, Data collection, Structure summary