+Open data
-Basic information
Entry | Database: PDB / ID: 7xhb | ||||||
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Title | Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP | ||||||
Components |
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Keywords | TRANSLOCASE / SecA ATPase / membrane protein / protein translocation / TRANSLOCATE | ||||||
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 / SRP-dependent cotranslational protein targeting to membrane, translocation / protein import / signal sequence binding / protein transmembrane transporter activity / protein secretion ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / protein import / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) Geobacillus thermodenitrificans NG80-2 (bacteria) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å | ||||||
Authors | Dong, L. / Li, L. | ||||||
Funding support | China, 1items
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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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xhb.cif.gz | 240.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xhb.ent.gz | 186.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/7xhb ftp://data.pdbj.org/pub/pdb/validation_reports/xh/7xhb | HTTPS FTP |
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-Related structure data
Related structure data | 33193MC 7xhaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein translocase subunit ... , 3 types, 3 molecules AYE
#1: Protein | Mass: 88673.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: secA / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P28366, protein-secreting ATPase |
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#2: Protein | Mass: 47628.238 Da / Num. of mol.: 1 / Mutation: G60C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans NG80-2 (bacteria) Strain: NG80-2 / Gene: secY / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A4IJK8 |
#3: Protein | Mass: 7030.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans NG80-2 (bacteria) Strain: NG80-2 / Gene: secE / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A4IJH4 |
-Protein , 1 types, 1 molecules B
#4: Protein | Mass: 37381.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 |
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-Non-polymers , 2 types, 2 molecules
#5: Chemical | ChemComp-MG / |
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#6: Chemical | ChemComp-ADP / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.18 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 57.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1083447 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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