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Yorodumi- PDB-4v8p: T.thermophila 60S ribosomal subunit in complex with initiation fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v8p | |||||||||
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Title | T.thermophila 60S ribosomal subunit in complex with initiation factor 6. | |||||||||
Components |
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Keywords | RIBOSOME / EUKARYOTIC INITIATION FACTOR 6 / EIF6 / 60S / TRANSLATION / LARGE RIBOSOMAL SUBUNIT / RRNA / RIBOSOMAL PROTEIN | |||||||||
Function / homology | Function and homology information ribosomal large subunit binding / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / large ribosomal subunit / ribosome biogenesis / ribosome binding / 5S rRNA binding / cytosolic large ribosomal subunit ...ribosomal large subunit binding / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / large ribosomal subunit / ribosome biogenesis / ribosome binding / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus / RNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | TETRAHYMENA THERMOPHILA (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å | |||||||||
Authors | Klinge, S. / Voigts-Hoffmann, F. / Leibundgut, M. / Arpagaus, S. / Ban, N. | |||||||||
Citation | Journal: Science / Year: 2011 Title: Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6. Authors: Klinge, S. / Voigts-Hoffmann, F. / Leibundgut, M. / Arpagaus, S. / Ban, N. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v8p.cif.gz | 14.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v8p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v8p_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 4v8p_full_validation.pdf.gz | 6.1 MB | Display | |
Data in XML | 4v8p_validation.xml.gz | 1.8 MB | Display | |
Data in CIF | 4v8p_validation.cif.gz | 2.5 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8p ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8p | HTTPS FTP |
-Related structure data
Related structure data | 1jj2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
-RNA chain , 3 types, 12 molecules A1D1F1H1B2C2E2G2B3C3E3G3
#1: RNA chain | Mass: 1084310.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: JN547815 #20: RNA chain | Mass: 49800.582 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: JN547815 #21: RNA chain | Mass: 38740.992 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: J01893 |
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-RIBOSOMAL PROTEIN ... , 4 types, 16 molecules AADAFAHAAMDMFMHMBBCBEBGBBLCLELGL
#2: Protein | Mass: 10703.564 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ24 #12: Protein | Mass: 13804.006 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23BV5 #23: Protein | Mass: 44348.539 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: O96774 #33: Protein | Mass: 24134.201 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22A30 |
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+Protein , 28 types, 108 molecules ABDBFBHBAEDEFEHEAFDFFFHFAGDGFGHGAHDHFHHHAJDJFJHJAKDKFKHKALDL...
-60S RIBOSOMAL PROTEIN ... , 12 types, 48 molecules ACDCFCHCAQDQFQHQBDCDEDGDBECEEEGEBHCHEHGHBICIEIGIBKCKEKGKBMCM...
#4: Protein | Mass: 12786.319 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22X38 #16: Protein | Mass: 11703.105 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q24F59 #25: Protein | Mass: 19754.959 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P24119 #26: Protein | Mass: 21373.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22AX5 #29: Protein | Mass: 24511.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q235M8 #30: Protein | Mass: 22641.775 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ15 #32: Protein | Mass: 16662.867 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q00454 #34: Protein | Mass: 34525.941 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q231U7 #37: Protein | Mass: 18164.055 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23TC8 #43: Protein | Mass: 27670.322 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ13 #44: Protein | Mass: 12990.064 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22DH9 #45: Protein | Mass: 15347.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q236T0 |
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-Non-polymers , 3 types, 6075 molecules
#48: Chemical | ChemComp-MG / #49: Chemical | ChemComp-ZN / #50: Water | ChemComp-HOH / | |
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-Details
Sequence details | UBIQUITIN FUSION, UBIQUITIN NOT VISIBLE IN STRUCTURE FOR CHAIN K. THE ENTRY 4A18 CONTAINS THE ...UBIQUITIN FUSION, UBIQUITIN NOT VISIBLE IN STRUCTURE FOR CHAIN K. THE ENTRY 4A18 CONTAINS THE PROTEINS THAT ARE DESCRIBED WITH LOWER CASE CHAIN IDS IN THE CITATION. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 55 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.52→40 Å / Num. obs: 1192534 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 96.88 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3.52→3.72 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JJ2 Resolution: 3.52→19.998 Å / SU ML: 0.89 / σ(F): 1.99 / Phase error: 24.46 / Stereochemistry target values: ML / Details: CHAIN G IS MODELLED AS UNK OF PDB ENTRY 1ZAX
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Solvent computation | Shrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.324 Å2 / ksol: 0.316 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.2 Å2
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Refinement step | Cycle: LAST / Resolution: 3.52→19.998 Å
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Refine LS restraints |
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LS refinement shell |
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