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Yorodumi- PDB-4v5o: CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v5o | |||||||||
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Title | CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH INITIATION FACTOR 1. | |||||||||
Components |
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Keywords | RIBOSOME / TRANSLATION | |||||||||
Function / homology | Function and homology information kinase activity / small ribosomal subunit / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | TETRAHYMENA THERMOPHILA (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.93 Å | |||||||||
Authors | Rabl, J. / Leibundgut, M. / Ataide, S.F. / Haag, A. / Ban, N. | |||||||||
Citation | Journal: Science / Year: 2011 Title: Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1. Authors: Rabl, J. / Leibundgut, M. / Ataide, S.F. / Haag, A. / Ban, N. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2C" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2C" 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 "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 "QA" 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v5o.cif.gz | 3.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v5o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v5o_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4v5o_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 4v5o_validation.xml.gz | 643.7 KB | Display | |
Data in CIF | 4v5o_validation.cif.gz | 891.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/4v5o ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v5o | HTTPS FTP |
-Related structure data
Related structure data | 2j02 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-RIBOSOMAL PROTEIN ... , 9 types, 18 molecules A1B1A5B5ADBDAEBEAGBGAHBHAJBJAQBQAUBU
#1: Protein | Mass: 7628.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q234G5 #5: Protein | Mass: 13844.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23PT4, UniProt: E6PBU4*PLUS #13: Protein | Mass: 21190.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q230V2 #14: Protein | Mass: 33743.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23KG1 #16: Protein | Mass: 22513.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22WU7 #17: Protein | Mass: 14931.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q238Q8 #19: Protein | Mass: 13696.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22DC6 #26: Protein | Mass: 18142.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22B78 #30: Protein | Mass: 13832.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22W26 |
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-40S RIBOSOMAL PROTEIN ... , 4 types, 8 molecules A2B2A4B4ALBLAWBW
#2: Protein | Mass: 24250.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22AV0 #4: Protein | Mass: 29709.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23DE3 #21: Protein | Mass: 15777.714 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P06147 #32: Protein | Mass: 29643.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0C233 |
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+Protein , 21 types, 42 molecules A3B3A6B6A7B7A8B8A9B9ABBBACBCAFBFAIBIAKBKAMBMANBNAOBOAPBPARBR...
-RNA chain , 1 types, 2 molecules AABA
#10: RNA chain | Mass: 565193.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: X56165 |
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-Non-polymers , 3 types, 1296 molecules
#36: Chemical | ChemComp-MG / #37: Chemical | ChemComp-ZN / #38: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | HEXACOORDINATED MAGNESIUM ION (MO6): HEXACOORDINATED MAGNESIUM ION REFINED IN HEXACOORDINATED FORM. ...HEXACOORDI |
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Sequence details | RESIDUES 697-704 OF THE 18S RRNA WERE NOT BUILT. RESIDUES 145-169 WERE BUILT AS POLY-SERINE AND ...RESIDUES 697-704 OF THE 18S RRNA WERE NOT BUILT. RESIDUES 145-169 WERE BUILT AS POLY-SERINE AND DEPOSITED AS UNK RESIDUES. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 71 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 50MM MES-KOH PH6.5, 80MM MGCL2, 200MM KCL, 0.495MM PUTRESCEINE, 4.4-5.4% (W/V) PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS / Detector: PIXEL / Date: Mar 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.93→100 Å / Num. obs: 364651 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.93→4.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.05 / % possible all: 61 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 2J02 2j02 Resolution: 3.93→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 25089988.51 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: REGION 697-704 OF THE 18S RRNA (CHAINS AA AND BA) WAS OMITTED FROM THE MODEL DUE TO DISORDER. (RESIDUES 145-169 OF RPS31E (CHAINS A9 AND B9) WERE BUILT AND REFINED AS POLY-SER.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 81.5375 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 148.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.93→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.93→4.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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