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- PDB-9oin: The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 13 -

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Basic information

Entry
Database: PDB / ID: 9oin
TitleThe von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragment 13
Components
  • (Elongin-C) x 2
  • Elongin-B
  • von Hippel-Lindau disease tumor suppressor
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 / intracellular membraneless organelle ...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 / 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 / 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 / protein serine/threonine kinase binding / negative regulation of autophagy / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription initiation at RNA polymerase II promoter / 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 / DNA-binding transcription factor binding / molecular adaptor activity / 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: 2.41 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)175,19413
Polymers174,97412
Non-polymers2191
Water1448
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor


Theoretical massNumber of molelcules
Total (without water)43,8223
Polymers43,8223
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-39 kcal/mol
Surface area15660 Å2
MethodPISA
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area15580 Å2
MethodPISA
3
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor


Theoretical massNumber of molelcules
Total (without water)43,7183
Polymers43,7183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-41 kcal/mol
Surface area15630 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)43,9374
Polymers43,7183
Non-polymers2191
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-39 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.044, 94.044, 363.683
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

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Protein , 4 types, 12 molecules ADGJBCFILEHK

#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.: 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: 11135.650 Da / Num. of mol.: 1
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: 20833.514 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: 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.: 3
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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Non-polymers , 2 types, 9 molecules

#5: Chemical ChemComp-A1CBJ / 1-(propan-2-yl)-4-[(pyridin-2-yl)methyl]piperazine


Mass: 219.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.39 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 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 PILATUS3 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: 2.41→49.08 Å / Num. obs: 64429 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.064 / Net I/σ(I): 11.2
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.516 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 64429 / CC1/2: 0.239 / Rpim(I) all: 1.516 / % 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: 2.41→49.08 Å / SU ML: 0.4232 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.0986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2827 3163 4.93 %
Rwork0.2328 60956 -
obs0.2353 64119 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.42 Å2
Refinement stepCycle: LAST / Resolution: 2.41→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10337 0 16 8 10361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008810613
X-RAY DIFFRACTIONf_angle_d1.033314464
X-RAY DIFFRACTIONf_chiral_restr0.05511670
X-RAY DIFFRACTIONf_plane_restr0.01011875
X-RAY DIFFRACTIONf_dihedral_angle_d18.60573868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.450.37651370.37382542X-RAY DIFFRACTION98.78
2.45-2.480.40571490.36242584X-RAY DIFFRACTION99.06
2.48-2.520.42461230.36162572X-RAY DIFFRACTION99.48
2.52-2.570.4271480.35592604X-RAY DIFFRACTION99.67
2.57-2.620.38111320.34152621X-RAY DIFFRACTION99.85
2.62-2.670.42861400.3512595X-RAY DIFFRACTION99.82
2.67-2.720.39421370.33012592X-RAY DIFFRACTION99.85
2.72-2.780.37351260.33132673X-RAY DIFFRACTION100
2.78-2.840.37591440.332593X-RAY DIFFRACTION99.85
2.84-2.910.3341280.30512629X-RAY DIFFRACTION99.86
2.91-2.990.34411400.26572596X-RAY DIFFRACTION99.78
2.99-3.080.35051460.27512626X-RAY DIFFRACTION99.82
3.08-3.180.33681230.27142668X-RAY DIFFRACTION99.93
3.18-3.290.3281310.26092617X-RAY DIFFRACTION99.89
3.29-3.430.30911230.25462674X-RAY DIFFRACTION99.93
3.43-3.580.29291280.25052677X-RAY DIFFRACTION99.89
3.58-3.770.30421550.23362640X-RAY DIFFRACTION99.86
3.77-4.010.24271400.20012646X-RAY DIFFRACTION99.82
4.01-4.320.24281360.17972697X-RAY DIFFRACTION99.86
4.32-4.750.20281430.16742707X-RAY DIFFRACTION99.86
4.75-5.440.231360.18032706X-RAY DIFFRACTION99.82
5.44-6.850.26521420.22882781X-RAY DIFFRACTION99.56
6.85-49.080.21831560.19092916X-RAY DIFFRACTION98.37
Refinement TLS params.Method: refined / Origin x: 11.8423606795 Å / Origin y: -29.8426556898 Å / Origin z: -23.8710594189 Å
111213212223313233
T0.597002779278 Å20.0257050243918 Å2-0.0439135157046 Å2-0.385703595067 Å20.00434364482642 Å2--0.399943883055 Å2
L0.0498980626868 °2-0.0188085057906 °2-0.0406138064905 °2-0.181275772483 °20.0371131910858 °2---0.0587605878782 °2
S0.0251802864449 Å °0.0162290853379 Å °0.000843136429385 Å °-0.0347315321712 Å °-0.0324142256442 Å °-0.0112389932749 Å °-0.00312723951538 Å °0.0219159112393 Å °0.00882314288207 Å °
Refinement TLS groupSelection details: all

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