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Yorodumi- PDB-4v8z: Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v8z | |||||||||||||||||||||
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Title | Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex | |||||||||||||||||||||
Components |
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Keywords | RIBOSOME / RIBOSOME INITIATION COMPLEX / INITIATOR FACTOR EIF5B / SINGLE PARTICLE ANALYSIS | |||||||||||||||||||||
Function / homology | Function and homology information ribosome hibernation / triplex DNA binding / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / protein-synthesizing GTPase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway ...ribosome hibernation / triplex DNA binding / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / protein-synthesizing GTPase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / GDP-dissociation inhibitor activity / regulation of translational initiation / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / : / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / response to cycloheximide / telomeric DNA binding / mRNA destabilization / TOR signaling / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / positive regulation of protein kinase activity / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / translation initiation factor binding / maturation of SSU-rRNA / translation repressor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / translational initiation / : / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to amino acid starvation / ribosome assembly / telomere maintenance / translation initiation factor activity / ribosomal large subunit biogenesis / cytosolic ribosome assembly / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytoplasmic stress granule / small ribosomal subunit rRNA binding / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / negative regulation of translation / ribosome / rRNA binding / protein ubiquitination / structural constituent of ribosome / translation / G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / response to antibiotic / negative regulation of gene expression / GTPase activity / mRNA binding / ubiquitin protein ligase binding Similarity search - Function | |||||||||||||||||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||||||||||||||
Authors | Fernandez, I.S. / Bai, X.C. / Hussain, T. / Kelley, A.C. / Lorsch, J.R. / Ramakrishnan, V. / Scheres, S.H.W. | |||||||||||||||||||||
Citation | Journal: Science / Year: 2013 Title: Molecular architecture of a eukaryotic translational initiation complex. Authors: Israel S Fernández / Xiao-Chen Bai / Tanweer Hussain / Ann C Kelley / Jon R Lorsch / V Ramakrishnan / Sjors H W Scheres / Abstract: The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start ...The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes. | |||||||||||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v8z.cif.gz | 5.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v8z.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8z ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8z | HTTPS FTP |
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-Related structure data
Related structure data | 2422MC 2421C 4v8yC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+40S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules A0A1A2A3A4AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZ
-Protein , 5 types, 5 molecules A5A6A7BmCV
#6: Protein | Mass: 16559.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05759 |
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#7: Protein | Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38011 |
#8: Protein | Mass: 29052.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39015 |
#73: Protein | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P0CH08 |
#83: Protein | Mass: 65317.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P39730, UniProt: O26359 |
+60S RIBOSOMAL PROTEIN ... , 40 types, 40 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBd...
-60S ACIDIC RIBOSOMAL PROTEIN ... , 3 types, 3 molecules BqBrBs
#76: Protein | Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P05317 |
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#77: Protein/peptide | Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
#78: Protein/peptide | Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
-RNA chain , 6 types, 6 molecules B2B5B7B8CWCX
#79: RNA chain | Mass: 577937.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
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#80: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: GenBank: BK006945 |
#81: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: GenBank: AE016820 |
#82: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: GenBank: HQ026735 |
#84: RNA chain | Mass: 24422.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
#85: RNA chain | Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
-Non-polymers , 4 types, 443 molecules
#86: Chemical | ChemComp-ZN / #87: Chemical | ChemComp-MG / #88: Chemical | ChemComp-OHX / #89: Chemical | ChemComp-GCP / | |
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-Details
Sequence details | THESE ARE PARTS OF THE PROTEIN SEQUENCES MODELED AS UNK RESIDUES. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RECONSTRUCTION OF 80S- EIF5B-MET-ITRNAMET EUKARYOTIC TRANSLATION INITIATION COMPLEX WITH TRNA IN THE PI-SITE AND Type: RIBOSOME |
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Buffer solution | Name: 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT pH: 7.2 Details: 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Jan 15, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 79096 X / Nominal defocus max: 3900 nm / Nominal defocus min: 1900 nm / Cs: 2 mm |
Specimen holder | Temperature: 85 K |
Image recording | Electron dose: 16 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) |
Image scans | Num. digital images: 1012 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 6.6 Å / Num. of particles: 5143 / Actual pixel size: 1.77 Å Magnification calibration: CROSS-CORRELATION BETWEEN CRYO-EM MAP AND CRYSTAL STRUCTURE Details: USE A NEWLY DEVELOPED STATISTICAL MOVIE PROCESSING APPROACH TO COMPENSATE FOR BEAM-INDUCED MOVEMENT. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2422. (DEPOSITION ID: 11817). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Details: METHOD--RIGID-BODY FITTING | ||||||||||||
Refinement | Highest resolution: 6.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.6 Å
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