6R7L

Ribosome-bound SecYEG translocon in a nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6 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

Partially inserted nascent chain unzips the lateral gate of the Sec translocon.

Kater, L.Frieg, B.Berninghausen, O.Gohlke, H.Beckmann, R.Kedrov, A.

(2019) Embo Rep. --: e48191-e48191

  • DOI: 10.15252/embr.201948191

  • PubMed Abstract: 
  • The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information ...

    The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information on the complex in the lipid membrane is scarce. Here, we present a cryo-electron microscopy-based structure of bacterial translocon SecYEG in lipid nanodiscs and elucidate an early intermediate state upon insertion of the FtsQ anchor domain. Insertion of the short nascent chain causes initial displacements within the lateral gate of the translocon, where α-helices 2b, 7, and 8 tilt within the membrane core to "unzip" the gate at the cytoplasmic side. Molecular dynamics simulations demonstrate that the conformational change is reversed in the absence of the ribosome, and suggest that the accessory α-helices of SecE subunit modulate the lateral gate conformation. Site-specific cross-linking validates that the FtsQ nascent chain passes the lateral gate upon insertion. The structure and the biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology.


    Organizational Affiliation

    Gene Center Munich, Ludwig-Maximilian-University, Munich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute for Computing, Jülich Supercomputing Centre, Institute for Complex Systems - Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany.,Synthetic Membrane Systems, Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SecG
G
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
E
107N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecY
Y
443Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secY (prlA)
Find proteins for P0AGA2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGA2
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
E, G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6 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
German Research FoundationGermanyKE1879/3-1
German Research FoundationGermanyCRC 1208
European Research CouncilCRYOTRANSLATION

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Type: Data collection, Database references