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Yorodumi- PDB-5aff: Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aff | ||||||
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Title | Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site | ||||||
Components |
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Keywords | CHAPERONE / RIBOSOME BIOGENESIS / ALPHA SOLENOID. | ||||||
Function / homology | Function and homology information ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding / 5S rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding Similarity search - Function | ||||||
Biological species | CHAETOMIUM THERMOPHILUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.398 Å | ||||||
Authors | Calvino, F.R. / Kharde, S. / Wild, K. / Bange, G. / Sinning, I. | ||||||
Citation | Journal: Nat.Commun. / Year: 2015 Title: Symportin 1 Chaperones 5S Rnp Assembly During Ribosome Biogenesis by Occupying an Essential Rrna-Binding Site. Authors: Calvino, F.R. / Kharde, S. / Ori, A. / Hendricks, A. / Wild, K. / Kressler, D. / Bange, G. / Hurt, E. / Beck, M. / Sinning, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aff.cif.gz | 301.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aff.ent.gz | 247.5 KB | Display | PDB format |
PDBx/mmJSON format | 5aff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aff_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 5aff_full_validation.pdf.gz | 491.9 KB | Display | |
Data in XML | 5aff_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5aff_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/5aff ftp://data.pdbj.org/pub/pdb/validation_reports/af/5aff | HTTPS FTP |
-Related structure data
Related structure data | 3u5e 4gmoS 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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Unit cell |
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-Components
#1: Protein | Mass: 72162.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0S5S6 |
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#2: Protein/peptide | Mass: 6060.083 Da / Num. of mol.: 1 / Fragment: N-TERMINUS LINEAR MOTIF, UNP RESIDUES 1-41 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0SEG2 |
#3: Protein | Mass: 20119.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0SHQ2 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM ACETATE, 8% (V/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 30, 2012 / Details: PT COATED MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→49.29 Å / Num. obs: 13505 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 112.54 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.19 / % possible all: 98.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4GMO AND 3U5E, CHAIN J Resolution: 3.398→49.256 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 33.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.398→49.256 Å
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Refine LS restraints |
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LS refinement shell |
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