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- PDB-9oiq: The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 15 -

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Basic information

Entry
Database: PDB / ID: 9oiq
TitleThe von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 15
Components
  • (Elongin-B) x 3
  • (Elongin-C) x 2
  • (von Hippel-Lindau disease tumor ...) x 2
KeywordsPROTEIN TRANSPORT / VHL / E3 ligase / Fragment-based drug discovery
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, 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: 2.66 Å
AuthorsAmporndanai, K. / Katinas, J.M. / Chopra, A. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateAWD00000788 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: NMR-Based Fragment Screen of the von Hippel-Lindau Elongin C&B Complex.
Authors: Amporndanai, K. / Katinas, J.M. / Chopra, A. / Kayode, O. / Vadukoot, A.K. / Waterson, A.G. / Fesik, S.W.
History
DepositionMay 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)175,01714
Polymers174,66212
Non-polymers3542
Water41423
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor


Theoretical massNumber of molelcules
Total (without water)43,7183
Polymers43,7183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor


Theoretical massNumber of molelcules
Total (without water)43,7183
Polymers43,7183
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7914
Polymers43,6143
Non-polymers1771
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Elongin-B
K: Elongin-C
L: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7914
Polymers43,6143
Non-polymers1771
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.281, 94.281, 363.761
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "D" and (resid 1 through 18 or (resid 19...
d_3ens_1(chain "G" and (resid 1 through 28 or (resid 29...
d_4ens_1(chain "J" and (resid 1 through 18 or (resid 19...
d_1ens_2(chain "B" and ((resid 17 and (name N or name...
d_2ens_2(chain "E" and (resid 17 through 31 or (resid 32...
d_3ens_2(chain "H" and ((resid 17 and (name N or name...
d_4ens_2(chain "K" and (resid 17 through 31 or (resid 32...
d_1ens_3(chain "C" and ((resid 62 and (name N or name...
d_2ens_3(chain "F" and ((resid 62 and (name N or name...
d_3ens_3(chain "I" and (resid 62 through 63 or (resid 64...
d_4ens_3(chain "L" and (resid 62 through 63 or (resid 64...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETGLUGLUAA1 - 591 - 59
d_12ens_1GLYGLYPHEPHEAA61 - 7961 - 79
d_13ens_1ASPASPLEULEUAA83 - 8883 - 88
d_14ens_1ILEILEMETMETAA90 - 10390 - 103
d_21ens_1METMETGLUGLUDD1 - 591 - 59
d_22ens_1GLYGLYLEULEUDD61 - 8861 - 88
d_23ens_1ILEILEMETMETDD90 - 10390 - 103
d_31ens_1METMETGLUGLUGG1 - 591 - 59
d_32ens_1GLYGLYPHEPHEGG61 - 7961 - 79
d_33ens_1ASPASPLEULEUGG83 - 8883 - 88
d_34ens_1ILEILEMETMETGG90 - 10390 - 103
d_41ens_1METMETGLUGLUJJ1 - 591 - 59
d_42ens_1GLYGLYPHEPHEJJ61 - 7961 - 79
d_43ens_1ASPASPLEULEUJJ83 - 8883 - 88
d_44ens_1ILEILEMETMETJJ90 - 10390 - 103
d_11ens_2METMETASPASPBB17 - 1113 - 97
d_21ens_2METMETSERSEREE17 - 473 - 33
d_22ens_2ASNASNASPASPEE58 - 11144 - 97
d_31ens_2METMETSERSERHH17 - 473 - 33
d_32ens_2ASNASNASPASPHH58 - 11144 - 97
d_41ens_2METMETSERSERKK17 - 473 - 33
d_42ens_2ASNASNASPASPKK58 - 11144 - 97
d_11ens_3VALVALPHEPHECC62 - 7629 - 43
d_12ens_3ASNASNTHRTHRCC78 - 20245 - 169
d_21ens_3VALVALPHEPHEFF62 - 7629 - 43
d_22ens_3ASNASNTHRTHRFF78 - 20245 - 169
d_31ens_3VALVALPHEPHEII62 - 7629 - 43
d_32ens_3ASNASNTHRTHRII78 - 20245 - 169
d_41ens_3VALVALPHEPHELL62 - 7629 - 43
d_42ens_3ASNASNTHRTHRLL78 - 20245 - 169

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.999562375229, -0.0282265318139, 0.00884991116338), (0.0282488203046, 0.999598032475, -0.00240366891062), (-0.00877850654951, 0.00265261655573, 0.99995794984)47.8576547639, 4.41908896771, -0.279716120693
2given(0.99350024105, 0.0585264596378, -0.0976315756043), (-0.0602317520469, 0.998077505954, -0.0146091804939), (0.0965888558689, 0.020394745196, 0.995115393957)47.9544600988, -43.5399321841, 1.42773048566
3given(0.996339976411, 0.0427850153738, -0.0740006342175), (-0.0444769231147, 0.998781865898, -0.0213679119938), (0.0729962650783, 0.0245810254504, 0.997029246548)0.906061082666, -47.7779284818, 1.44687366018
4given(0.999836648718, -0.0178037604615, -0.00311480227464), (0.017816309369, 0.999833080308, 0.0040485358631), (0.00304220319008, -0.00410336881053, 0.999986953597)47.51633989, 4.62772856607, -0.131246518296
5given(0.991462814889, 0.0453798339599, -0.122238117471), (-0.0487649823126, 0.998501260814, -0.0248436843589), (0.120927512144, 0.0305925288631, 0.992189817517)47.0296646651, -43.708400024, 1.58947912103
6given(0.995811673132, 0.0300793589144, -0.0863385419261), (-0.0330055050579, 0.998921193818, -0.0326662697247), (0.0852628189218, 0.0353790998917, 0.995730169775)0.261884395577, -48.0539547492, 1.51593562992
7given(0.999616656671, 0.0133598500452, -0.0242498270619), (-0.0132346610872, 0.999898288647, 0.0053156473382), (0.0243183768305, -0.00499267137767, 0.999691797396)47.3384495867, 4.44943579968, -0.0930453398334
8given(0.996332641286, 0.0580945302675, -0.0628195308884), (-0.0598819098237, 0.997841520176, -0.0269528753222), (0.0611181215672, 0.0306157829438, 0.997660888805)48.2712345925, -43.7571537441, 1.1766658483
9given(0.997473434512, 0.0583672653421, -0.0404970341925), (-0.0597562824215, 0.997634458581, -0.0339804909116), (0.0384178884513, 0.0363145891884, 0.998601680581)1.22546335299, -48.3391834313, 1.23203019285

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Components

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Protein , 5 types, 8 molecules AJBEDGHK

#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: 11852.389 Da / Num. of mol.: 2
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: 11135.650 Da / Num. of mol.: 2
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
#4: 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: 11748.406 Da / Num. of mol.: 1
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
#6: 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: 11852.390 Da / Num. of mol.: 1
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
#7: 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: 11031.668 Da / Num. of mol.: 2
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

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Von Hippel-Lindau disease tumor ... , 2 types, 4 molecules CILF

#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 20729.531 Da / Num. of mol.: 3
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
#5: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 20833.514 Da / Num. of mol.: 1
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

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Non-polymers , 2 types, 25 molecules

#8: Chemical ChemComp-A1CBM / 2-(5-amino-1H-1,3-benzimidazol-1-yl)ethan-1-ol


Mass: 177.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N3O / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate pH 5.5, 0.2 M magnesium acetate, 5 mM DTT and 14-20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→49.15 Å / Num. obs: 92676 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 51.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 18.9
Reflection shellResolution: 2.66→2.75 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 92676 / CC1/2: 0.813 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→49.15 Å / SU ML: 0.3565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 2433 5.05 %
Rwork0.2263 45766 -
obs0.2287 48199 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.87 Å2
Refinement stepCycle: LAST / Resolution: 2.66→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10302 0 26 23 10351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910568
X-RAY DIFFRACTIONf_angle_d1.193414398
X-RAY DIFFRACTIONf_chiral_restr0.06561666
X-RAY DIFFRACTIONf_plane_restr0.0141857
X-RAY DIFFRACTIONf_dihedral_angle_d18.54553840
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.560553826929
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.666331253743
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.600207793989
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.562715207542
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.793256363783
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.716017295832
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.654923238961
ens_3d_3CCX-RAY DIFFRACTIONTorsion NCS0.819697531854
ens_3d_4CCX-RAY DIFFRACTIONTorsion NCS0.761193666427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.710.34841200.34112658X-RAY DIFFRACTION99.93
2.71-2.770.35731450.30162666X-RAY DIFFRACTION100
2.77-2.840.34971310.28642635X-RAY DIFFRACTION100
2.84-2.910.29591420.28522638X-RAY DIFFRACTION99.89
2.91-2.990.32441400.26022653X-RAY DIFFRACTION100
2.99-3.080.31131560.2652639X-RAY DIFFRACTION99.93
3.08-3.170.34311480.25952680X-RAY DIFFRACTION99.96
3.17-3.290.29941310.2582649X-RAY DIFFRACTION99.93
3.29-3.420.30911470.26312680X-RAY DIFFRACTION99.96
3.42-3.570.33381430.25682674X-RAY DIFFRACTION99.96
3.58-3.760.36651490.29452597X-RAY DIFFRACTION96.28
3.76-40.28081520.21892653X-RAY DIFFRACTION99.08
4-4.310.23651570.18472711X-RAY DIFFRACTION99.76
4.31-4.740.17671360.15772733X-RAY DIFFRACTION99.9
4.74-5.430.24521470.17252738X-RAY DIFFRACTION99.86
5.43-6.830.23231450.2242802X-RAY DIFFRACTION99.49
6.83-49.150.2251440.19782960X-RAY DIFFRACTION98.54
Refinement TLS params.Method: refined / Origin x: 11.6811083076 Å / Origin y: -30.008261707 Å / Origin z: -23.603174396 Å
111213212223313233
T0.619075443818 Å20.0221603887474 Å2-0.0959558144064 Å2-0.297020118428 Å20.00295465182409 Å2--0.384042983654 Å2
L0.108899020249 °20.006896615822 °2-0.0394080086825 °2-0.142287391774 °20.0173351664469 °2---0.0660615044002 °2
S0.0289995017631 Å °0.0339260995788 Å °-0.00775318521455 Å °-0.0710208233919 Å °-0.0306293635539 Å °-0.0316288841496 Å °0.00698490013145 Å °0.00499079476204 Å °0.00423182558395 Å °
Refinement TLS groupSelection details: all

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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