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Yorodumi- PDB-6itc: Structure of a substrate engaged SecA-SecY protein translocation ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6itc | |||||||||
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Title | Structure of a substrate engaged SecA-SecY protein translocation machine | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / SecA / SecY / Translocation / Cryo-EM | |||||||||
Function / homology | Function and homology information outer membrane protein complex / cell envelope Sec protein transport complex / protein-exporting ATPase activity / monoatomic ion transmembrane transporter activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / detection of virus / protein import / outer membrane ...outer membrane protein complex / cell envelope Sec protein transport complex / protein-exporting ATPase activity / monoatomic ion transmembrane transporter activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / detection of virus / protein import / outer membrane / porin activity / pore complex / protein transmembrane transporter activity / protein secretion / protein targeting / monoatomic ion transport / bioluminescence / generation of precursor metabolites and energy / cell outer membrane / outer membrane-bounded periplasmic space / symbiont entry into host cell / membrane raft / DNA damage response / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) Geobacillus thermodenitrificans (bacteria) Lama glama (llama) Escherichia coli (E. coli) Aequorea victoria (jellyfish) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
Authors | Ma, C.Y. / Wu, X.F. / Sun, D.J. / Park, E.Y. / Rapoport, T.A. / Gao, N. / Long, L. | |||||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structure of the substrate-engaged SecA-SecY protein translocation machine. Authors: Chengying Ma / Xiaofei Wu / Dongjie Sun / Eunyong Park / Marco A Catipovic / Tom A Rapoport / Ning Gao / Long Li / Abstract: The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are ...The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY channel by the SecA ATPase. How a polypeptide is moved through the SecA-SecY complex is poorly understood, as structural information is lacking. Here, we report an electron cryo-microscopy (cryo-EM) structure of a translocating SecA-SecY complex in a lipid environment. The translocating polypeptide chain can be traced through both SecA and SecY. In the captured transition state of ATP hydrolysis, SecA's two-helix finger is close to the polypeptide, while SecA's clamp interacts with the polypeptide in a sequence-independent manner by inducing a short β-strand. Taking into account previous biochemical and biophysical data, our structure is consistent with a model in which the two-helix finger and clamp cooperate during the ATPase cycle to move a polypeptide through the channel. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6itc.cif.gz | 321.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6itc.ent.gz | 253.7 KB | Display | PDB format |
PDBx/mmJSON format | 6itc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/6itc ftp://data.pdbj.org/pub/pdb/validation_reports/it/6itc | HTTPS FTP |
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-Related structure data
Related structure data | 9731MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-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: 88916.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: secA, div+, BSU35300 / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): #1/H766 / References: UniProt: P28366 |
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#2: Protein | Mass: 46768.301 Da / Num. of mol.: 1 / Mutation: G60C,Q202T,L210G,F211G,R213N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria) Strain: NG80-2 / Gene: secY, GTNG_0125 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A4IJK8 |
#3: Protein | Mass: 8249.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria) Strain: NG80-2 / Gene: secE, GTNG_0091 / Production host: Escherichia coli (E. coli) / References: UniProt: A4IJH4 |
-Protein , 2 types, 2 molecules BG
#5: Protein | Mass: 6024.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A910*PLUS |
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#6: Protein | Mass: 26813.113 Da / Num. of mol.: 1 / Mutation: Q80R,F99S,M153T,V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
-Antibody , 2 types, 2 molecules VC
#4: Antibody | Mass: 12919.544 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#7: Antibody | Mass: 12368.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 4 types, 5 molecules
#8: Chemical | ChemComp-MG / |
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#9: Chemical | ChemComp-BEF / |
#10: Chemical | ChemComp-ADP / |
#11: Chemical |
-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 | Name: SecA-SecY complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | 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 FIELDBright-field microscopy |
Image recording | Electron dose: 5 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130153 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |