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- PDB-1vcb: THE VHL-ELONGINC-ELONGINB STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1vcb
TitleTHE VHL-ELONGINC-ELONGINB STRUCTURE
Components
  • PROTEIN (ELONGIN B)
  • PROTEIN (ELONGIN C)
  • PROTEIN (VHL)
KeywordsTRANSCRIPTION / TUMOR SUPPRESSOR / CANCER / UBIQUITIN / BETA SANDWICH / TRANSCRIPTIONAL ELONGATION
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 / Replication of the SARS-CoV-1 genome / VCB complex / 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 / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / 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 / protein serine/threonine kinase binding / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / cilium / 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 / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain ...von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsStebbins, C.E. / Kaelin, W.G. / Pavletich, N.P.
CitationJournal: Science / Year: 1999
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.
History
DepositionMar 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ELONGIN B)
B: PROTEIN (ELONGIN C)
C: PROTEIN (VHL)
D: PROTEIN (ELONGIN B)
E: PROTEIN (ELONGIN C)
F: PROTEIN (VHL)
G: PROTEIN (ELONGIN B)
H: PROTEIN (ELONGIN C)
I: PROTEIN (VHL)
J: PROTEIN (ELONGIN B)
K: PROTEIN (ELONGIN C)
L: PROTEIN (VHL)


Theoretical massNumber of molelcules
Total (without water)176,76412
Polymers176,76412
Non-polymers00
Water8,179454
1
A: PROTEIN (ELONGIN B)
B: PROTEIN (ELONGIN C)
C: PROTEIN (VHL)


Theoretical massNumber of molelcules
Total (without water)44,1913
Polymers44,1913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-35 kcal/mol
Surface area16240 Å2
MethodPISA
2
D: PROTEIN (ELONGIN B)
E: PROTEIN (ELONGIN C)
F: PROTEIN (VHL)


Theoretical massNumber of molelcules
Total (without water)44,1913
Polymers44,1913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-35 kcal/mol
Surface area16250 Å2
MethodPISA
3
G: PROTEIN (ELONGIN B)
H: PROTEIN (ELONGIN C)
I: PROTEIN (VHL)


Theoretical massNumber of molelcules
Total (without water)44,1913
Polymers44,1913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-35 kcal/mol
Surface area16210 Å2
MethodPISA
4
J: PROTEIN (ELONGIN B)
K: PROTEIN (ELONGIN C)
L: PROTEIN (VHL)


Theoretical massNumber of molelcules
Total (without water)44,1913
Polymers44,1913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-34 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 93.500, 362.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Cell settingtetragonal
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999322, 0.034116, -0.013802), (-0.034228, 0.999382, -0.007982), (0.013521, 0.008449, 0.999873)5.3001, -49.0671, 1.03758
2given(0.998645, -0.049028, 0.017463), (0.050565, 0.993452, -0.102454), (-0.012326, 0.103198, 0.994584)-44.69755, -53.85593, 6.1099
3given(0.998765, -0.033083, 0.037069), (0.03541, 0.997322, -0.063992), (-0.034853, 0.065225, 0.997262)-46.61111, -5.28696, 2.91031
4given(0.999712, 0.022652, -0.00796), (-0.022692, 0.99973, -0.004917), (0.007846, 0.005096, 0.999956)5.04411, -48.33294, 0.57616
5given(0.998394, -0.047997, 0.03009), (0.051053, 0.99254, -0.110717), (-0.024551, 0.112075, 0.993396)-43.96524, -54.35083, 6.0178
6given(0.998598, -0.034531, 0.040121), (0.037698, 0.995995, -0.081065), (-0.037161, 0.082464, 0.995901)-46.63693, -5.97568, 3.85965
7given(0.999822, 0.018842, -0.000988), (-0.018852, 0.99976, -0.011177), (0.000777, 0.011193, 0.999937)5.37235, -48.58498, 0.58597
8given(0.998509, -0.035688, 0.041301), (0.039942, 0.993431, -0.107238), (-0.037202, 0.108728, 0.993375)-42.25394, -54.74003, 5.242
9given(0.998204, -0.037722, 0.046545), (0.0412, 0.996244, -0.076165), (-0.043497, 0.077946, 0.996008)-46.24837, -5.45145, 3.24
10given(0.999691, -0.02473, -0.002306), (0.024673, 0.999457, -0.02181), (0.002844, 0.021746, 0.999759)2.89823, -48.05087, 1.2437
11given(0.99689, -0.072567, 0.03073), (0.07383, 0.996378, -0.042194), (-0.027557, 0.044331, 0.998637)-44.70386, -48.80565, 1.61886
12given(0.997681, -0.058134, 0.035393), (0.059381, 0.997612, -0.035262), (-0.033258, 0.037282, 0.998751)-47.95584, -1.75798, 1.20432

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Components

#1: Protein
PROTEIN (ELONGIN B)


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.) Homo sapiens (human) / Plasmid: PGEX-4T3 / Species (production host): Escherichia coli / Gene (production host): VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15370
#2: Protein
PROTEIN (ELONGIN C)


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.) Homo sapiens (human) / Plasmid: PBB75 / Species (production host): Escherichia coli / Gene (production host): VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15369
#3: Protein
PROTEIN (VHL)


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.) Homo sapiens (human) / Description: VHL(54-213) ALTERNATIVE ENDOGENOUS POLYPEPTIDE / Plasmid: PGEX-4T3 / Species (production host): Escherichia coli / Gene (production host): VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40337
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 43 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDDetails
112-17 %PEG80001reservoiror 10-15% PEG2000
20.2 Mmagnesium acetate1reservoir
35 mMdithiothreitol1reservoir
40.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 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

Software
NameVersionClassification
CCP4model building
RAVEmodel building
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RAVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1965 5 %RANDOM
Rwork0.238 ---
obs-38609 84.6 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 54.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10408 0 0 454 10862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS 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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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