- EMDB-33193: Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-33193
Title
Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP
Map data
Sample
Complex: Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.
Complex: SecA
Protein or peptide: Protein translocase subunit SecA
Complex: SecY
Protein or peptide: Protein translocase subunit SecY
Complex: SecE
Protein or peptide: Protein translocase subunit SecE
Complex: sfGFP
Protein or peptide: Translocating peptide
Ligand: MAGNESIUM ION
Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywords
SecA ATPase / membrane protein / protein translocation / TRANSLOCATE / TRANSLOCASE
Function / homology
Function and homology information
protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein secretion / protein transmembrane transporter activity ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein secretion / protein transmembrane transporter activity / protein targeting / membrane raft / ATP binding / metal ion binding / plasma membrane / cytosol Similarity search - Function
SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SEC-C motif / SecA P-loop domain / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain ...SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SEC-C motif / SecA P-loop domain / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / 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 / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecA Similarity search - Component
Biological species
Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Geobacillus thermodenitrificans NG80-2 (bacteria) / Escherichia coli (E. coli)
Method
single particle reconstruction / cryo EM / Resolution: 3.33 Å
National Natural Science Foundation of China (NSFC)
31870835
China
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structural basis of SecA-mediated protein translocation. Authors: Linlin Dong / Song Yang / Jingxia Chen / Xiaofei Wu / Dongjie Sun / Chen Song / Long Li / Abstract: Secretory proteins are cotranslationally or posttranslationally translocated across lipid membranes via a protein-conducting channel named SecY in prokaryotes and Sec61 in eukaryotes. The vast ...Secretory proteins are cotranslationally or posttranslationally translocated across lipid membranes via a protein-conducting channel named SecY in prokaryotes and Sec61 in eukaryotes. The vast majority of secretory proteins in bacteria are driven through the channel posttranslationally by SecA, a highly conserved ATPase. How a polypeptide chain is moved by SecA through the SecY channel is poorly understood. Here, we report electron cryomicroscopy structures of the active SecA-SecY translocon with a polypeptide substrate. The substrate is captured in different translocation states when clamped by SecA with different nucleotides. Upon binding of an ATP analog, SecA undergoes global conformational changes to push the polypeptide substrate toward the channel in a way similar to how the RecA-like helicases translocate their nucleic acid substrates. The movements of the polypeptide substrates in the SecA-SecY translocon share a similar structural basis to those in the ribosome-SecY complex during cotranslational translocation.
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.
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.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
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.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
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