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- PDB-9ipw: Crystal structure of VHL-EloB-EloC in complex with a fragment com... -

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Basic information

Entry
Database: PDB / ID: 9ipw
TitleCrystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3)
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsPROTEIN BINDING / E3 ligase / 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: 3 Å
AuthorsLee, B.I. / Kim, Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Other government
CitationJournal: To Be Published
Title: Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3)
Authors: Lee, B.I. / Kim, Y.
History
DepositionJul 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 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)167,15513
Polymers166,94912
Non-polymers2061
Water362
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor


Theoretical massNumber of molelcules
Total (without water)41,7373
Polymers41,7373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-34 kcal/mol
Surface area15820 Å2
MethodPISA
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor


Theoretical massNumber of molelcules
Total (without water)41,7373
Polymers41,7373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-31 kcal/mol
Surface area15790 Å2
MethodPISA
3
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor


Theoretical massNumber of molelcules
Total (without water)41,7373
Polymers41,7373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-40 kcal/mol
Surface area16280 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)41,9434
Polymers41,7373
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-40 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.443, 94.443, 361.486
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: EloB / 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: EloC / 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
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#4: Chemical ChemComp-A1L2Z / 7-Hydroxy-4-methoxymethylcoumarin / 4-(methoxymethyl)-7-oxidanyl-chromen-2-one


Mass: 206.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 8K,0.1M Na cacodylate-HCl pH 6.0, 0.2M Mg acetate, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 62450 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 60.72 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.46
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 10053 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8zv8

8zv8


Resolution: 3→49.06 Å / SU ML: 0.4601 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2728 3689 5.92 %
Rwork0.2065 58646 -
obs0.2104 62335 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.88 Å2
Refinement stepCycle: LAST / Resolution: 3→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10206 0 15 2 10223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110446
X-RAY DIFFRACTIONf_angle_d1.281414160
X-RAY DIFFRACTIONf_chiral_restr0.06261595
X-RAY DIFFRACTIONf_plane_restr0.01181823
X-RAY DIFFRACTIONf_dihedral_angle_d7.24861383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.35941450.30992245X-RAY DIFFRACTION96.53
3.04-3.080.3871350.27172198X-RAY DIFFRACTION99.96
3.08-3.130.36111450.26742289X-RAY DIFFRACTION99.96
3.13-3.170.30681490.26112262X-RAY DIFFRACTION100
3.17-3.220.28111410.26082223X-RAY DIFFRACTION100
3.22-3.270.29981400.24032295X-RAY DIFFRACTION99.96
3.27-3.330.36281380.22942245X-RAY DIFFRACTION100
3.33-3.390.30051470.22962277X-RAY DIFFRACTION100
3.39-3.460.3211390.23342260X-RAY DIFFRACTION99.96
3.46-3.530.31341460.23142248X-RAY DIFFRACTION99.96
3.53-3.60.31651440.22542285X-RAY DIFFRACTION100
3.6-3.690.26011370.22322232X-RAY DIFFRACTION99.96
3.69-3.780.26881480.20612290X-RAY DIFFRACTION99.92
3.78-3.880.31211370.19232237X-RAY DIFFRACTION99.92
3.88-40.21531410.20072257X-RAY DIFFRACTION99.92
4-4.130.2591460.1872259X-RAY DIFFRACTION99.92
4.13-4.270.25321480.17452266X-RAY DIFFRACTION99.88
4.27-4.440.21371360.17072257X-RAY DIFFRACTION99.92
4.44-4.650.24591440.16912267X-RAY DIFFRACTION99.88
4.65-4.890.22911350.17122256X-RAY DIFFRACTION99.83
4.89-5.20.24391440.17892262X-RAY DIFFRACTION100
5.2-5.60.23971450.19652257X-RAY DIFFRACTION99.88
5.6-6.160.28761430.23182244X-RAY DIFFRACTION99.67
6.16-7.050.32931420.23282265X-RAY DIFFRACTION99.67
7.05-8.870.21811460.19622263X-RAY DIFFRACTION100
8.87-49.060.27491280.18732207X-RAY DIFFRACTION97.05

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