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Yorodumi- PDB-2c9w: CRYSTAL STRUCTURE OF SOCS-2 IN COMPLEX WITH ELONGIN-B AND ELONGIN... -
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-Basic information
Entry | Database: PDB / ID: 2c9w | ||||||
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Title | CRYSTAL STRUCTURE OF SOCS-2 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 1.9A RESOLUTION | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATION / GROWTH REGULATION / SH2 DOMAIN / SIGNAL TRANSDUCTION INHIBITOR / NUCLEAR PROTEIN / TRANSCRIPTION / UBL CONJUGATION PATHWAY | ||||||
Function / homology | Function and homology information JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / growth hormone receptor signaling pathway / negative regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphatidylinositol phosphate biosynthetic process / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / regulation of signal transduction / mammary gland alveolus development / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Growth hormone receptor signaling / cellular response to hormone stimulus / Negative regulation of FLT3 / RNA Polymerase II Pre-transcription Events / insulin-like growth factor receptor binding / positive regulation of neuron differentiation / lactation / Interleukin-7 signaling / transcription corepressor binding / regulation of cell growth / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / response to estradiol / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / protein ubiquitination / intracellular signal transduction / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Debreczeni, J.E. / Bullock, A. / Amos, A. / Savitsky, P. / Barr, A. / Burgess, N. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Knapp, S. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2006 Title: Crystal structure of the SOCS2-elongin C-elongin B complex defines a prototypical SOCS box ubiquitin ligase. Authors: Bullock, A.N. / Debreczeni, J.E. / Edwards, A.M. / Sundstrom, M. / Knapp, S. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c9w.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c9w.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 2c9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9w ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9w | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19273.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: O14508 |
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-TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 2 types, 2 molecules BC
#2: Protein | Mass: 13147.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370 |
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#3: Protein | Mass: 10974.616 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369 |
-Non-polymers , 3 types, 178 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | SOCS FAMILY PROTEINS PARTICIPATE AT THE CLASSICAL NEGATIVE FEEDBACK SYSTEM THAT REGULATES CYTOKINE ...SOCS FAMILY PROTEINS PARTICIPAT |
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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: 2.7 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 2M AMSO4 0.2M NACL, 0.1M CACODYLATE PH 6.5 300 NL SITTING DROPS AT 4 DEGREES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.90008 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 18, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90008 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.25 Å / Num. obs: 395240 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 11.6 % / Rmerge(I) obs: 0.0726 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 11.19 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.29 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1O4H, 1LM8 Resolution: 1.9→91.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.738 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→91.29 Å
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Refine LS restraints |
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