+Open data
-Basic information
Entry | Database: PDB / ID: 3zrf | ||||||
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Title | pVHL54-213-EloB-EloC complex_apo | ||||||
Components |
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Keywords | TRANSCRIPTION / TUMOUR SUPRESSOR PROTEIN / CHRONIC ANEAMIA TREATMENT / E3 UBIQUITIN LIGASE | ||||||
Function / homology | Function and homology information regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to hypoxia / regulation of gene expression / Neddylation / protein-macromolecule adaptor activity / Replication of the SARS-CoV-2 genome / DNA-binding transcription factor binding / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / amyloid fibril formation / molecular adaptor activity / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Van Molle, I. / Buckley, D.L. / Crews, C.M. / Ciulli, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Targeting the Von Hippel-Lindau E3 Ubiquitin Ligase Using Small Molecules to Disrupt the Vhl/Hif-1Alpha Interaction Authors: Buckley, D.L. / Van Molle, I. / Gareiss, P.C. / Tae, H.S. / Michel, J. / Noblin, D.J. / Jorgensen, W.L. / Ciulli, A. / Crews, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zrf.cif.gz | 265.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zrf.ent.gz | 212.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zrf_validation.pdf.gz | 522.4 KB | Display | wwPDB validaton report |
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Full document | 3zrf_full_validation.pdf.gz | 579.8 KB | Display | |
Data in XML | 3zrf_validation.xml.gz | 52.7 KB | Display | |
Data in CIF | 3zrf_validation.cif.gz | 72.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/3zrf ftp://data.pdbj.org/pub/pdb/validation_reports/zr/3zrf | HTTPS FTP |
-Related structure data
Related structure data | 3zrcC 1vcbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 13147.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370 #2: Protein | Mass: 10974.616 Da / Num. of mol.: 4 / Fragment: 17-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369 #3: Protein | Mass: 18840.438 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40337 #4: Water | ChemComp-HOH / | Sequence details | PVHL ISOFORM 3, STARTING FROM RESIDUE 54 RESIDUES 51-53 CONSEQUENCE OF EXPRESSION TAG. STARTING AT ...PVHL ISOFORM 3, STARTING FROM RESIDUE 54 RESIDUES 51-53 CONSEQUENC | |
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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: 2.72 Å3/Da / Density % sol: 54.42 % / Description: NONE |
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Crystal grow | Details: 0.1 M NA CACODYLATE PH 5.8, 0.2 M MG ACETATE, 15% PEG8000, 5MM DTT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2010 |
Radiation | Monochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 74099 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.8→2.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.87 / % possible all: 92.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VCB Resolution: 2.8→46.54 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.854 / SU B: 19.529 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.289 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→46.54 Å
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Refine LS restraints |
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