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- PDB-9rp9: Crystal structure of mouse pVHL-ElonginB-ElonginC complex -

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Basic information

Entry
Database: PDB / ID: 9rp9
TitleCrystal structure of mouse pVHL-ElonginB-ElonginC complex
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / Complex / E3 ligase / VBC / Protein degradation
Function / homology
Function and homology information


regulation of catecholamine metabolic process / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Neddylation / target-directed miRNA degradation / VCB complex ...regulation of catecholamine metabolic process / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Neddylation / target-directed miRNA degradation / VCB complex / elongin complex / Antigen processing: Ubiquitination & Proteasome degradation / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / transcription corepressor binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / neuron differentiation / ubiquitin-dependent protein catabolic process / response to ethanol / response to hypoxia / protein ubiquitination / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / cytosol
Similarity search - Function
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 ...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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
IODIDE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Elongin-B / Elongin-C / von Hippel-Lindau disease tumor suppressor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBlat, A. / Biterova, E. / Cukier, C.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other private Poland
CitationJournal: To Be Published
Title: Crystal structure of mouse pVHL-ElonginB-ElonginC complex
Authors: Blat, A. / Biterova, E. / Cukier, C.
History
DepositionJun 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: von Hippel-Lindau disease tumor suppressor
B: Elongin-B
C: Elongin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,69612
Polymers41,8113
Non-polymers8859
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex (43.5 kDa) migartes on HPLC-SEC as ovalbumin (43 kDa)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-25 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.480, 59.780, 91.670
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein von Hippel-Lindau disease tumor suppressor / pVHL


Mass: 19019.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vhl, Vhlh / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3TTE7
#2: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11816.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Elob, Tceb2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62869
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Stromal membrane-associated protein SMAP1B homolog / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eloc, Tceb1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P83940

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Non-polymers , 5 types, 135 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.36855 Å3/Da / Density % sol: 48.10174 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20 mM Hepes, pH 7.5, 100 mM NaCl, 1 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.1→46.04 Å / Num. obs: 22839 / % possible obs: 99.5 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.058 / Rrim(I) all: 0.082 / Χ2: 1.03 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1779 / CC1/2: 0.55 / Rpim(I) all: 0.559 / Rrim(I) all: 0.791 / Χ2: 0.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS0.6.7.1data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.04 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.768 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22172 1142 5 %RANDOM
Rwork0.18246 ---
obs0.18447 21696 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.478 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å2-1.78 Å2
2---1.22 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 36 126 2923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122865
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162765
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.8613871
X-RAY DIFFRACTIONr_angle_other_deg0.5681.7626383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2895342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.925528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66110499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9453.421368
X-RAY DIFFRACTIONr_mcbond_other2.9363.421368
X-RAY DIFFRACTIONr_mcangle_it4.1646.1191704
X-RAY DIFFRACTIONr_mcangle_other4.1636.1191705
X-RAY DIFFRACTIONr_scbond_it4.5873.961497
X-RAY DIFFRACTIONr_scbond_other4.5863.9621498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6577.022166
X-RAY DIFFRACTIONr_long_range_B_refined7.82634.843109
X-RAY DIFFRACTIONr_long_range_B_other7.8134.843095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 80 -
Rwork0.282 1529 -
obs--94.2 %

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