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Yorodumi- EMDB-1762: Cryo-EM structure of the E. coli translating ribosome in complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1762 | |||||||||
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Title | Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor | |||||||||
Map data | E. coli translating ribosome in complex with SRP and its receptor | |||||||||
Sample |
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Keywords | Ribosome / Co-translational Targeting / Signal Recognition Particle / FtsY | |||||||||
Function / homology | Function and homology information endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity ...endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.5 Å | |||||||||
Authors | Estrozi LF / Boehringer D / Shan S-O / Ban N / Schaffitzel C | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2011 Title: Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor. Authors: Leandro F Estrozi / Daniel Boehringer / Shu-Ou Shan / Nenad Ban / Christiane Schaffitzel / Abstract: We report the 'early' conformation of the Escherichia coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome, as determined by cryo-EM. FtsY binds to the ...We report the 'early' conformation of the Escherichia coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome, as determined by cryo-EM. FtsY binds to the tetraloop of the SRP RNA, whereas the NG domains of the SRP protein and FtsY interact weakly in this conformation. Our results suggest that optimal positioning of the SRP RNA tetraloop and the Ffh NG domain leads to FtsY recruitment. | |||||||||
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_1762.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-1762-v30.xml emd-1762.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | 1762.png | 185.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1762 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1762 | HTTPS FTP |
-Validation report
Summary document | emd_1762_validation.pdf.gz | 237.1 KB | Display | EMDB validaton report |
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Full document | emd_1762_full_validation.pdf.gz | 236.2 KB | Display | |
Data in XML | emd_1762_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1762 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1762 | HTTPS FTP |
-Related structure data
Related structure data | 2xkvMC 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_1762.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E. coli translating ribosome in complex with SRP and its receptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.81 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-nascent chain-SRP-FtsY complex
Entire | Name: Ribosome-nascent chain-SRP-FtsY complex |
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Components |
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-Supramolecule #1000: Ribosome-nascent chain-SRP-FtsY complex
Supramolecule | Name: Ribosome-nascent chain-SRP-FtsY complex / type: sample / ID: 1000 Oligomeric state: One SRP-FtsY complex bound to 70S ribosome Number unique components: 3 |
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Molecular weight | Theoretical: 2.65 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.5 MDa |
-Macromolecule #1: Signal Recognition Particle Protein
Macromolecule | Name: Signal Recognition Particle Protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 145 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Signal recognition particle protein |
-Macromolecule #2: Cell division protein FtsY
Macromolecule | Name: Cell division protein FtsY / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 145 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Signal recognition particle receptor FtsY |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.32 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Hepes-KOH, 100 mM KOAc, 8 mM Mg(OAc)2 |
Grid | Details: Carbon-coated lacey formvar grids |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 28822 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: CNS |
Refinement | Space: REAL |
Output model | PDB-2xkv: |