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- EMDB-9731: Structure of a substrate engaged SecA-SecY protein translocation ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9731 | |||||||||
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Title | Structure of a substrate engaged SecA-SecY protein translocation machine | |||||||||
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![]() | SecA / SecY / Translocation / Cryo-EM / PROTEIN TRANSPORT | |||||||||
Function / homology | ![]() outer membrane protein complex / protein-exporting ATPase activity / cell envelope Sec protein transport complex / monoatomic ion transmembrane transporter activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / detection of virus / outer membrane / protein import ...outer membrane protein complex / protein-exporting ATPase activity / cell envelope Sec protein transport complex / monoatomic ion transmembrane transporter activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / detection of virus / outer membrane / protein import / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / porin activity / pore complex / protein secretion / protein transmembrane transporter activity / 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 / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
![]() | Ma CY / Wu XF | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
Images | ![]() | 55.7 KB | ||
Filedesc metadata | ![]() | 7.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 389.4 KB | Display | ![]() |
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Full document | ![]() | 389 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6itcMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : SecA-SecY complex
+Supramolecule #1: SecA-SecY complex
+Macromolecule #1: Protein translocase subunit SecA
+Macromolecule #2: Protein translocase subunit SecY
+Macromolecule #3: Protein translocase subunit SecE
+Macromolecule #4: Nanobody
+Macromolecule #5: Translocating peptide
+Macromolecule #6: Green fluorescent protein
+Macromolecule #7: Nanobody
+Macromolecule #8: MAGNESIUM ION
+Macromolecule #9: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #11: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 5.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130153 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6itc: |