|Entry||Database: PDB / ID: 6r7l|
|Title||Ribosome-bound SecYEG translocon in a nanodisc|
|Keywords||MEMBRANE PROTEIN / monomeric translocon / nanodisc / insertion intermediate|
|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 / SRP-dependent cotranslational protein targeting to membrane, translocation / intracellular protein transmembrane transport / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / signal sequence binding / protein transmembrane transporter activity / protein targeting / protein secretion ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / SRP-dependent cotranslational protein targeting to membrane, translocation / intracellular protein transmembrane transport / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / signal sequence binding / protein transmembrane transporter activity / protein targeting / protein secretion / intracellular protein transport / integral component of plasma membrane / integral component of membrane / plasma membrane
SecE superfamily / SecY conserved site / Protein translocase subunit SecY / SecY domain superfamily / SecE subunit of protein translocation complex, bacterial-like / SecY/SEC61-alpha family / Protein translocase complex, SecE/Sec61-gamma subunit
Protein translocase subunit SecE / Protein translocase subunit SecE / Protein translocase subunit SecY
|Biological species||Escherichia coli (E. coli)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å|
|Authors||Kater, L. / Beckmann, R. / Kedrov, A.|
|Funding support|| Germany, 3items |
|Citation||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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
E: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
Y: Protein translocase subunit SecY
|#1: Protein/peptide|| |
Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
|#2: Protein|| |
Mass: 10880.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A377BMD6, UniProt: P0AG96*PLUS
|#3: Protein|| |
Mass: 48553.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AGA2
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc|
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 7.4|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 2.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 13098|
|Image scans||Width: 4096 / Height: 4096|
|CTF correction||Type: NONE|
|Particle selection||Num. of particles selected: 837184|
|Symmetry||Point symmetry: C1 (asymmetric)|
|3D reconstruction||Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112366 / Algorithm: FOURIER SPACE / Symmetry type: POINT|
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.:Changes in new EM Navigator and Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi