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- PDB-2v24: Structure of the human SPRY domain-containing SOCS box protein SSB-4 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v24 | ||||||
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Title | Structure of the human SPRY domain-containing SOCS box protein SSB-4 | ||||||
![]() | SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4 | ||||||
![]() | PROTEIN BINDING / PROTEIN-BINDING | ||||||
Function / homology | ![]() positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / Antigen processing: Ubiquitination & Proteasome degradation / rhythmic process / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction ...positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / Antigen processing: Ubiquitination & Proteasome degradation / rhythmic process / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Uppenberg, J. / Bullock, A. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Ugochukwu, E. / Bunkoczi, G. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. ...Uppenberg, J. / Bullock, A. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Ugochukwu, E. / Bunkoczi, G. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Knapp, S. | ||||||
![]() | ![]() 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. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.2 KB | Display | ![]() |
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PDB format | ![]() | 72.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2jk9C ![]() 3emwC ![]() 3f2oC ![]() 2fnjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22756.725 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST TWO RESIDUES REMAIN FROM A CLEAVED HIS6 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 6.5 Details: 0.1 M NACACOD PH6.5, 14.4% PEG10K, 0.16 M CAAC2, 20% GLYCEROL, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2007 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.1 Å / Num. obs: 13208 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2FNJ Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 16.377 / SU ML: 0.212 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.209 / 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: 23.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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