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- PDB-9qe5: VCB in complex with VHL-binding compound 82 -

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Basic information

Entry
Database: PDB / ID: 9qe5
TitleVCB in complex with VHL-binding compound 82
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / protac / degrader / complex / e3 ligase / vhl / vcb
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / Cul2-RING ubiquitin ligase complex / 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 / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / negative regulation of signal transduction / 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 / protein serine/threonine kinase binding / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / cell morphogenesis / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / Neddylation / microtubule cytoskeleton / regulation of gene expression / Replication of the SARS-CoV-2 genome / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / molecular adaptor activity / cellular response to hypoxia / 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 / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / 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
: / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBraun, M.B. / Dierlamm, N. / Hartmann, M.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Breaking Barriers in PROTAC Design: Improving Solubility of USP7-Targeting Degraders
Authors: Wittenburg, S. / Zuleeg, M.R. / Peter, K. / Lemnitzer, P. / Voget, R. / Bricelj, A. / Gobec, M. / Dierlamm, N. / Braun, M.B. / Geiger, T.M. / Heim, C. / Stakemeier, A. / Wagner, K.G. / ...Authors: Wittenburg, S. / Zuleeg, M.R. / Peter, K. / Lemnitzer, P. / Voget, R. / Bricelj, A. / Gobec, M. / Dierlamm, N. / Braun, M.B. / Geiger, T.M. / Heim, C. / Stakemeier, A. / Wagner, K.G. / Nowak, R.P. / Hartmann, M.D. / Sosic, I. / Guetschow, M. / Kroenke, J. / Steinebach, C.
History
DepositionMar 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 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: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor
J: Elongin-B
K: Elongin-C
L: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,14016
Polymers196,02512
Non-polymers2,1154
Water724
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5354
Polymers49,0063
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-39 kcal/mol
Surface area16460 Å2
MethodPISA
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5354
Polymers49,0063
Non-polymers5291
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-40 kcal/mol
Surface area16360 Å2
MethodPISA
3
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5354
Polymers49,0063
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-38 kcal/mol
Surface area16780 Å2
MethodPISA
4
J: Elongin-B
K: Elongin-C
L: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5354
Polymers49,0063
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-40 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.215, 94.215, 366.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

#1: 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: 14914.768 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#2: 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 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein
von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 23116.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#4: Chemical
ChemComp-A1I58 / (2~{S},4~{R})-1-[(2~{S})-1-(1-fluoranylcyclopropyl)carbonylpiperidin-2-yl]carbonyl-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 528.639 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33FN4O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.1 M sodium cacodylate pH 5.7, 0.2 M magnesium acetate, 12% (w/v) PEG 3350, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.1 Å / Num. obs: 58240 / % possible obs: 99.6 % / Redundancy: 26.7 % / Biso Wilson estimate: 64.33 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.17
Reflection shellResolution: 2.5→2.65 Å / Num. unique obs: 9182 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.72 Å / SU ML: 0.4345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.5594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2726 1560 2.69 %
Rwork0.2452 56393 -
obs0.246 57953 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.81 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10631 0 148 4 10783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007511033
X-RAY DIFFRACTIONf_angle_d1.249815019
X-RAY DIFFRACTIONf_chiral_restr0.07541717
X-RAY DIFFRACTIONf_plane_restr0.00851936
X-RAY DIFFRACTIONf_dihedral_angle_d15.52171513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.47781390.40285011X-RAY DIFFRACTION99.77
2.58-2.670.37261410.33445064X-RAY DIFFRACTION99.81
2.67-2.780.32911410.31345079X-RAY DIFFRACTION99.85
2.78-2.910.35591380.30445033X-RAY DIFFRACTION99.63
2.91-3.060.39331400.29755078X-RAY DIFFRACTION99.62
3.06-3.250.31581410.28565104X-RAY DIFFRACTION99.7
3.25-3.50.29941420.2725113X-RAY DIFFRACTION99.75
3.5-3.860.34971360.27734949X-RAY DIFFRACTION96.67
3.86-4.410.23291440.21035195X-RAY DIFFRACTION99.79
4.41-5.560.22821470.20185279X-RAY DIFFRACTION99.82
5.56-45.720.20591510.20825488X-RAY DIFFRACTION98.9

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