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Yorodumi- EMDB-1217: Signal recognition particle receptor exposes the ribosomal transl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1217 | |||||||||
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Title | Signal recognition particle receptor exposes the ribosomal translocon binding site. | |||||||||
Map data | a | |||||||||
Sample |
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Function / homology | Function and homology information SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / granulocyte differentiation / signal recognition particle binding / cotranslational protein targeting to membrane / signal-recognition-particle GTPase / protein targeting to ER ...SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / granulocyte differentiation / signal recognition particle binding / cotranslational protein targeting to membrane / signal-recognition-particle GTPase / protein targeting to ER / XBP1(S) activates chaperone genes / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / cytoplasmic microtubule / SRP-dependent cotranslational protein targeting to membrane / neutrophil chemotaxis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / intracellular protein transport / GDP binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / nuclear speck / structural constituent of ribosome / translation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular exosome / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Triticum sp. (plant) / Canis sp. (mammal) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
Authors | Halic M | |||||||||
Citation | Journal: Science / Year: 2006 Title: Signal recognition particle receptor exposes the ribosomal translocon binding site. Authors: Mario Halic / Marco Gartmann / Oliver Schlenker / Thorsten Mielke / Martin R Pool / Irmgard Sinning / Roland Beckmann / Abstract: Signal sequences of secretory and membrane proteins are recognized by the signal recognition particle (SRP) as they emerge from the ribosome. This results in their targeting to the membrane by ...Signal sequences of secretory and membrane proteins are recognized by the signal recognition particle (SRP) as they emerge from the ribosome. This results in their targeting to the membrane by docking with the SRP receptor, which facilitates transfer of the ribosome to the translocon. Here, we present the 8 angstrom cryo-electron microscopy structure of a "docking complex" consisting of a SRP-bound 80S ribosome and the SRP receptor. Interaction of the SRP receptor with both SRP and the ribosome rearranged the S domain of SRP such that a ribosomal binding site for the translocon, the L23e/L35 site, became exposed, whereas Alu domain-mediated elongation arrest persisted. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1217.map.gz | 16.9 MB | EMDB map data format | |
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Header (meta data) | emd-1217-v30.xml emd-1217.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | 1217.gif | 23.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1217 | HTTPS FTP |
-Validation report
Summary document | emd_1217_validation.pdf.gz | 341.8 KB | Display | EMDB validaton report |
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Full document | emd_1217_full_validation.pdf.gz | 341.3 KB | Display | |
Data in XML | emd_1217_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1217 | HTTPS FTP |
-Related structure data
Related structure data | 2go5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1217.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | a | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ribosome-SRP-SR
Entire | Name: ribosome-SRP-SR |
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Components |
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-Supramolecule #1000: ribosome-SRP-SR
Supramolecule | Name: ribosome-SRP-SR / type: sample / ID: 1000 / Number unique components: 3 |
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-Supramolecule #1: 80s
Supramolecule | Name: 80s / type: complex / ID: 1 / Name.synonym: 80s / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Triticum sp. (plant) / synonym: Bread wheat |
-Macromolecule #1: SRP
Macromolecule | Name: SRP / type: protein_or_peptide / ID: 1 / Name.synonym: SRP / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Canis sp. (mammal) / synonym: dog |
-Macromolecule #2: SRP receptor
Macromolecule | Name: SRP receptor / type: protein_or_peptide / ID: 2 / Name.synonym: SR / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Canis sp. (mammal) / synonym: dog |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE |
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-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 1.23 µm |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: gg / Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider |
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-Atomic model buiding 1
Software | Name: situs |
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Details | Protocol: Rigid Body |
Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-2go5: |