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Yorodumi- EMDB-1063: Structure of the signal recognition particle interacting with the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1063 | |||||||||
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Title | Structure of the signal recognition particle interacting with the elongation-arrested ribosome. | |||||||||
Map data | Structure of signal recognition particle interacting with elongation arested ribosome | |||||||||
Sample |
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Function / homology | Function and homology information signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / granulocyte differentiation / absorption of visible light / signal recognition particle binding / G protein-coupled opsin signaling pathway / signal recognition particle ...signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / granulocyte differentiation / absorption of visible light / signal recognition particle binding / G protein-coupled opsin signaling pathway / signal recognition particle / photoreceptor inner segment membrane / 11-cis retinal binding / cotranslational protein targeting to membrane / G protein-coupled photoreceptor activity / signal-recognition-particle GTPase / negative regulation of translational elongation / protein targeting to ER / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / photoreceptor outer segment membrane / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / visual perception / neutrophil chemotaxis / photoreceptor disc membrane / secretory granule lumen / ficolin-1-rich granule lumen / nuclear body / nuclear speck / GTPase activity / Neutrophil degranulation / nucleolus / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular region / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Canis lupus familiaris (dog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Halic M / Beckmann R | |||||||||
Citation | Journal: Nature / Year: 2004 Title: Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Authors: Mario Halic / Thomas Becker / Martin R Pool / Christian M T Spahn / Robert A Grassucci / Joachim Frank / Roland Beckmann / Abstract: Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal ...Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal recognition particle (SRP), an evolutionarily conserved ribonucleoprotein particle. SRP recognizes signal sequences of nascent protein chains emerging from the ribosome. Subsequent binding of SRP leads to a pause in peptide elongation and to the ribosome docking to the membrane-bound SRP receptor. Here we present the structure of a targeting complex consisting of mammalian SRP bound to an active 80S ribosome carrying a signal sequence. This structure, solved to 12 A by cryo-electron microscopy, enables us to generate a molecular model of SRP in its functional conformation. The model shows how the S domain of SRP contacts the large ribosomal subunit at the nascent chain exit site to bind the signal sequence, and that the Alu domain reaches into the elongation-factor-binding site of the ribosome, explaining its elongation arrest activity. | |||||||||
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_1063.map.gz | 7.9 MB | EMDB map data format | |
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Header (meta data) | emd-1063-v30.xml emd-1063.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | 1063.gif | 11.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1063 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1063 | HTTPS FTP |
-Validation report
Summary document | emd_1063_validation.pdf.gz | 333.2 KB | Display | EMDB validaton report |
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Full document | emd_1063_full_validation.pdf.gz | 332.7 KB | Display | |
Data in XML | emd_1063_validation.xml.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1063 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1063 | HTTPS FTP |
-Related structure data
Related structure data | 1ry1MC 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_1063.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of signal recognition particle interacting with elongation arested ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.26 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 : 80S RNC-SRP complex fron canis sp.
Entire | Name: 80S RNC-SRP complex fron canis sp. |
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Components |
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-Supramolecule #1000: 80S RNC-SRP complex fron canis sp.
Supramolecule | Name: 80S RNC-SRP complex fron canis sp. / type: sample / ID: 1000 / Oligomeric state: one srp binds one ribosome / Number unique components: 3 |
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-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Name.synonym: 80S RNC / Details: q / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Canis lupus familiaris (dog) / synonym: Dog |
Molecular weight | Experimental: 4 MDa / Theoretical: 4 MDa |
-Macromolecule #1: mammalian SRP
Macromolecule | Name: mammalian SRP / type: ligand / ID: 1 / Name.synonym: SRP / Details: q / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Canis lupus familiaris (dog) / Strain: beagle / synonym: Dog / Tissue: pancreas / Cell: secretory cells / Organelle: ER / Location in cell: ER |
Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa |
Recombinant expression | Organism: Canis lupus familiaris (dog) |
-Macromolecule #2: tRNA
Macromolecule | Name: tRNA / type: ligand / ID: 2 / Name.synonym: tRNA / Details: q / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Canis lupus familiaris (dog) / synonym: Dog |
Molecular weight | Experimental: 25 KDa / Theoretical: 25 KDa |
Recombinant expression | Organism: wheat germ (plant) |
-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 | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.3 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider |
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-Atomic model buiding 1
Details | The domains were separately fitted by manual docking using program O |
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Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-1ry1: |