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Yorodumi- PDB-3emw: Crystal Structure of human splA/ryanodine receptor domain and SOC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3emw | ||||||
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Title | Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 2 (SPSB2) in complex with a 20-residue VASA peptide | ||||||
Components |
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Keywords | APOPTOSIS / Apoptosis nucleus / UBL conjugation pathwayc / CL transcription regulation / Transcription / Phosphoprotein / Ubl conjugation pathway / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information posterior cell cortex / secondary piRNA processing / gamete generation / P granule / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / ubiquitin-like ligase-substrate adaptor activity / protein localization ...posterior cell cortex / secondary piRNA processing / gamete generation / P granule / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / ubiquitin-like ligase-substrate adaptor activity / protein localization / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA helicase activity / cell differentiation / intracellular signal transduction / RNA helicase / protein ubiquitination / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Filippakopoulos, P. / Sharpe, T. / Keates, T. / Murray, J.W. / Savitsky, P. / Roos, A.K. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Filippakopoulos, P. / Sharpe, T. / Keates, T. / Murray, J.W. / Savitsky, P. / Roos, A.K. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural basis for Par-4 recognition by the SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4. Authors: Filippakopoulos, P. / Low, A. / Sharpe, T.D. / Uppenberg, J. / Yao, S. / Kuang, Z. / Savitsky, P. / Lewis, R.S. / Nicholson, S.E. / Norton, R.S. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3emw.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3emw.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 3emw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3emw_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 3emw_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 3emw_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3emw_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3emw ftp://data.pdbj.org/pub/pdb/validation_reports/em/3emw | HTTPS FTP |
-Related structure data
Related structure data | 2jk9SC 2v24C 3f2oC S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 23849.627 Da / Num. of mol.: 1 / Fragment: UNP residues 26-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB2, GRCC9, SSB2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q99619 | ||
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#2: Protein/peptide | Mass: 2497.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P09052*PLUS | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.178M Na/KPO4, 17.8% PEG3350, 8.88% EtGly, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975653 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975653 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.83 Å / Num. obs: 24366 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.22 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3494 / Rsym value: 0.618 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JK9 Resolution: 1.8→42.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.491 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.523 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→42.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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