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Open data
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Basic information
Entry | Database: PDB / ID: 1vcb | ||||||
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Title | THE VHL-ELONGINC-ELONGINB STRUCTURE | ||||||
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![]() | TRANSCRIPTION / TUMOR SUPPRESSOR / CANCER / UBIQUITIN / BETA SANDWICH / TRANSCRIPTIONAL ELONGATION | ||||||
Function / homology | ![]() 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 elongation by RNA polymerase II / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / 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 / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Neddylation / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / 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 DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stebbins, C.E. / Kaelin, W.G. / Pavletich, N.P. | ||||||
![]() | ![]() Title: Structure of the VHL-ElonginC-ElonginB complex: implications for VHL tumor suppressor function. Authors: Stebbins, C.E. / Kaelin Jr., W.G. / Pavletich, N.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276 KB | Display | ![]() |
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PDB format | ![]() | 224.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.2 KB | Display | ![]() |
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Full document | ![]() | 486.5 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 49.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 13147.781 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-120 Source method: isolated from a genetically manipulated source Details: DISORDERED RESIDUES: 99-120 / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 12485.135 Da / Num. of mol.: 4 / Fragment: RESIDUES 17-112 Source method: isolated from a genetically manipulated source Details: DISORDERED RESIDUES: 50-57 / Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 18558.162 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-213 Source method: isolated from a genetically manipulated source Details: DISORDERED RESIDUES: 54-62, 205-213 / Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.7 Details: 10-15% PEG 2000, 200MM MAGNESIUM ACETATE, 100MM SODIUM CACODYLATE PH 5.7 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 41219 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Rsym value: 7 |
Reflection | *PLUS Num. measured all: 123622 / Rmerge(I) obs: 0.07 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS (500KCAL MOL^-1 ANGSTROM^-2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 54.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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