- EMDB-4743: Ribosome-bound SecYEG translocon in a nanodisc -
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Basic information
Entry
Database: EMDB / ID: EMD-4743
Title
Ribosome-bound SecYEG translocon in a nanodisc
Map data
SecYEG:Nanodisc portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement.
Sample
Complex: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
Protein or peptide: SecG
Protein or peptide: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
Protein or peptide: Protein translocase subunit SecY
Keywords
monomeric translocon / nanodisc / insertion intermediate / MEMBRANE PROTEIN
Function / homology
Function and homology information
protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein secretion / protein transmembrane transporter activity / protein targeting ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein secretion / protein transmembrane transporter activity / protein targeting / intracellular protein transport / membrane => GO:0016020 / membrane / plasma membrane Similarity search - Function
SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily ...SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecE / Protein translocase subunit SecY Similarity search - Component
Biological species
Escherichia coli (E. coli)
Method
single particle reconstruction / cryo EM / Resolution: 6.0 Å
Journal: EMBO Rep / Year: 2019 Title: Partially inserted nascent chain unzips the lateral gate of the Sec translocon. Authors: Lukas Kater / Benedikt Frieg / Otto Berninghausen / Holger Gohlke / Roland Beckmann / Alexej Kedrov / 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 ...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.
History
Deposition
Mar 29, 2019
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Header (metadata) release
Aug 7, 2019
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Map release
Aug 7, 2019
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Update
May 22, 2024
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Current status
May 22, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. This map includes the tRNA, nascent chain, SecYEG and nanodisc. Filtered according to local resolution.
Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. This map includes the tRNA, nascent chain, SecYEG and nanodisc. Filtered according to local resolution.
Entire : Stalled E. coli ribosome nascent chain complex (RNC) bound to the...
Entire
Name: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
Components
Complex: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
Protein or peptide: SecG
Protein or peptide: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
Protein or peptide: Protein translocase subunit SecY
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Supramolecule #1: Stalled E. coli ribosome nascent chain complex (RNC) bound to the...
Supramolecule
Name: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)
Organism: Escherichia coli (E. coli)
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Macromolecule #1: SecG
Macromolecule
Name: SecG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
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