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- PDB-8qjs: VHL/Elongin B/Elongin C complex with compound 155 -

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Basic information

Entry
Database: PDB / ID: 8qjs
TitleVHL/Elongin B/Elongin C complex with compound 155
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / VHL / ELONGIN / VBC / E3 LIGASE / VON HIPPEL-LINDAU / UBIQUITINASE
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
Chem-VL6 / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.191 Å
AuthorsKerry, P.S. / Hole, A.J. / Perez-Dorado, J.I.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2024
Title: PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models.
Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / ...Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / Gordon, D. / Hamman, B.D. / Harbin, A. / Haskell, R. / He, M. / Hole, A.J. / Januario, T. / Kerry, P.S. / Koenig, S.G. / Li, L. / Merchant, M. / Perez-Dorado, I. / Pizzano, J. / Quinn, C. / Rose, C.M. / Rousseau, E. / Soto, L. / Staben, L.R. / Sun, H. / Tian, Q. / Wang, J. / Wang, W. / Ye, C.S. / Ye, X. / Zhang, P. / Zhou, Y. / Yauch, R. / Dragovich, P.S.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)168,10416
Polymers165,70112
Non-polymers2,4034
Water27015
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0264
Polymers41,4253
Non-polymers6011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-40 kcal/mol
Surface area16890 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)42,0264
Polymers41,4253
Non-polymers6011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-41 kcal/mol
Surface area16630 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)42,0264
Polymers41,4253
Non-polymers6011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-38 kcal/mol
Surface area16760 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)42,0264
Polymers41,4253
Non-polymers6011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-39 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.235, 93.235, 361.904
Angle α, β, γ (deg.)90, 90, 90
Int Tables number91
Space group name H-MP4122

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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: 11748.406 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: 18702.291 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-VL6 / (2S,4R)-1-[(2R)-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 600.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H40N4O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Sodium Citrate pH 6.0, 200 mM Magnesium Acetate, 50 mM DTT, 14% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9121 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9121 Å / Relative weight: 1
ReflectionResolution: 3.018→48.76 Å / Num. obs: 27684 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.1
Reflection shellResolution: 3.018→3.25 Å / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1355 / CC1/2: 1

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.191→48.74 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.552
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 1397 -RANDOM
Rwork0.2542 ---
obs0.2552 27350 98.7 %-
Displacement parametersBiso mean: 73.49 Å2
Baniso -1Baniso -2Baniso -3
1--5.865 Å20 Å20 Å2
2---5.865 Å20 Å2
3---11.73 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3.191→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10846 0 168 15 11029
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00611269HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8715296HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3958SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1881HARMONIC5
X-RAY DIFFRACTIONt_it11269HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1463SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8300SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion16.37
LS refinement shellResolution: 3.191→3.21 Å
RfactorNum. reflection% reflection
Rfree0.2927 18 -
Rwork0.3382 --
obs--98.18 %

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