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- PDB-8zv8: Crystal structure of VHL-EloB-EloC in complex with a fragment com... -

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Basic information

Entry
Database: PDB / ID: 8zv8
TitleCrystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_2 (D7)
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsPROTEIN BINDING / E3 ligase / PROTAC / VHL / EloB / EloC
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: 2.46 Å
AuthorsLee, B.I. / Kim, Y. / Baek, S.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Other government2210340 Korea, Republic Of
Other government2310200 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_2 (D7)
Authors: Kim, Y. / Baek, S.J. / Lee, B.I.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)167,71816
Polymers166,94912
Non-polymers7694
Water1,62190
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9294
Polymers41,7373
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-35 kcal/mol
Surface area15730 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)41,9294
Polymers41,7373
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-33 kcal/mol
Surface area15910 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)41,9294
Polymers41,7373
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-43 kcal/mol
Surface area16430 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)41,9294
Polymers41,7373
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-41 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.896, 93.896, 364.118
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: 11956.372 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: residue 1-104, no fusion tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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
Details: residue 17-112, no fusion tag, additional Met at N-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein
von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18806.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: residue 54-213, Histag at N-terminus was cleaved by TEV protease.
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#4: Chemical
ChemComp-A1L2C / 4-(hydroxymethyl)-7-oxidanyl-chromen-2-one


Mass: 192.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 8K, 0.1 M Na cacodylate-HCl pH 6.0, 0.2 M Mg acetate, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 60319 / % possible obs: 99.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 33.04 Å2 / CC1/2: 0.996 / Rsym value: 0.092 / Net I/σ(I): 18.736
Reflection shellResolution: 2.46→2.5 Å / Num. unique obs: 2955 / CC1/2: 0.86 / Rsym value: 0.555

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZRF

3zrf


Resolution: 2.46→38.13 Å / SU ML: 0.3599 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2866 3543 3.33 %
Rwork0.2348 102739 -
obs0.2365 60319 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.34 Å2
Refinement stepCycle: LAST / Resolution: 2.46→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10206 0 56 90 10352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002910490
X-RAY DIFFRACTIONf_angle_d0.52714222
X-RAY DIFFRACTIONf_chiral_restr0.04191595
X-RAY DIFFRACTIONf_plane_restr0.0041826
X-RAY DIFFRACTIONf_dihedral_angle_d5.95641386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.490.3257980.32252738X-RAY DIFFRACTION63.2
2.49-2.530.40621070.29433119X-RAY DIFFRACTION70.89
2.53-2.570.37091110.28713325X-RAY DIFFRACTION77.13
2.57-2.610.3471220.29113734X-RAY DIFFRACTION83.7
2.61-2.650.37261390.28783908X-RAY DIFFRACTION90.94
2.65-2.70.38681390.28954176X-RAY DIFFRACTION94.98
2.7-2.750.35091490.28394250X-RAY DIFFRACTION97.93
2.75-2.80.34031490.27924265X-RAY DIFFRACTION98.33
2.8-2.860.30751480.28054296X-RAY DIFFRACTION98.43
2.86-2.920.34881470.28424357X-RAY DIFFRACTION99.1
2.92-2.980.32481440.27464276X-RAY DIFFRACTION99.3
2.98-3.060.32391470.27054326X-RAY DIFFRACTION99.03
3.06-3.140.35631490.2644359X-RAY DIFFRACTION99.12
3.14-3.230.31391510.26334346X-RAY DIFFRACTION99.05
3.23-3.340.35811460.25434327X-RAY DIFFRACTION99.16
3.34-3.460.35541530.24574298X-RAY DIFFRACTION99.24
3.46-3.60.30451520.24634337X-RAY DIFFRACTION99.14
3.6-3.760.29711580.22774369X-RAY DIFFRACTION99.54
3.76-3.960.23391480.2084259X-RAY DIFFRACTION98.7
3.96-4.210.23911460.1964294X-RAY DIFFRACTION98.43
4.21-4.530.21871470.17314238X-RAY DIFFRACTION97.57
4.53-4.980.19051520.17824272X-RAY DIFFRACTION97.51
4.99-5.70.2391450.20414259X-RAY DIFFRACTION97.5
5.71-7.180.26271500.23814304X-RAY DIFFRACTION98.43
7.18-38.130.2181460.20184307X-RAY DIFFRACTION98.67

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