+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33193 | |||||||||
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Title | Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein transmembrane transporter activity / protein secretion / protein targeting / membrane raft ...cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / 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 | single particle reconstruction / cryo EM / Resolution: 3.33 Å | |||||||||
Authors | Dong L / Li L | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33193.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-33193-v30.xml emd-33193.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
Images | emd_33193.png | 89.6 KB | ||
Others | emd_33193_half_map_1.map.gz emd_33193_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33193 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33193 | HTTPS FTP |
-Related structure data
Related structure data | 7xhbMC 7xhaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33193.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33193_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33193_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.
+Supramolecule #1: Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.
+Supramolecule #2: SecA
+Supramolecule #3: SecY
+Supramolecule #4: SecE
+Supramolecule #5: sfGFP
+Macromolecule #1: Protein translocase subunit SecA
+Macromolecule #2: Protein translocase subunit SecY
+Macromolecule #3: Protein translocase subunit SecE
+Macromolecule #4: Translocating peptide
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1083447 |