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Yorodumi- EMDB-1263: Following the signal sequence from ribosomal tunnel exit to signa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1263 | |||||||||
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Title | Following the signal sequence from ribosomal tunnel exit to signal recognition particle. | |||||||||
Map data | w | |||||||||
Sample |
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Function / homology | Function and homology information absorption of visible light / G protein-coupled photoreceptor activity / signal recognition particle / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane ...absorption of visible light / G protein-coupled photoreceptor activity / signal recognition particle / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / negative regulation of cytoplasmic translational initiation / photoreceptor outer segment membrane / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / visual perception / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / : / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / photoreceptor disc membrane / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.1 Å | |||||||||
Authors | Halic M / Blau M / Becker T / Mielke T / Pool MR / Wild K / Sinning I / Beckmann R | |||||||||
Citation | Journal: Nature / Year: 2006 Title: Following the signal sequence from ribosomal tunnel exit to signal recognition particle. Authors: Mario Halic / Michael Blau / Thomas Becker / Thorsten Mielke / Martin R Pool / Klemens Wild / Irmgard Sinning / Roland Beckmann / Abstract: Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal ...Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting. | |||||||||
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_1263.map.gz | 12 MB | EMDB map data format | |
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Header (meta data) | emd-1263-v30.xml emd-1263.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
Images | 1263.gif | 43 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1263 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1263 | HTTPS FTP |
-Related structure data
Related structure data | 2j28MC 1261C 1262C 1264C 2j37C 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_1263.map.gz / Format: CCP4 / Size: 94.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | w | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : E. coli signal recognition particle bound to ribosome nascent cha...
Entire | Name: E. coli signal recognition particle bound to ribosome nascent chain complex |
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Components |
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-Supramolecule #1000: E. coli signal recognition particle bound to ribosome nascent cha...
Supramolecule | Name: E. coli signal recognition particle bound to ribosome nascent chain complex type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: ribosome
Supramolecule | Name: ribosome / type: complex / ID: 1 / Details: nascent chain / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-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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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: 3.0 µm / Nominal defocus min: 0.9 µm |
Sample stage | Specimen holder: f / Specimen holder model: OTHER |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider |
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