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- PDB-6bvb: Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C -

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Basic information

Entry
Database: PDB / ID: 6bvb
TitleCrystal structure of HIF-2alpha-pVHL-elongin B-elongin C
Components
  • Elongin-B
  • Elongin-C
  • Hypoxia-Inducible Factor 2 alpha
  • von Hippel-Lindau disease tumor suppressor
KeywordsGENE REGULATION / E3 Ubiquitin Ligase
Function / homology
Function and homology information


myoblast fate commitment / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression / regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / norepinephrine metabolic process / transcription elongation factor activity ...myoblast fate commitment / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression / regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / norepinephrine metabolic process / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / surfactant homeostasis / epithelial cell maturation / Replication of the SARS-CoV-1 genome / VCB complex / Regulation of gene expression by Hypoxia-inducible Factor / 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 / blood vessel remodeling / embryonic placenta development / 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 / visual perception / negative regulation of autophagy / regulation of heart rate / protein serine/threonine kinase binding / Pexophagy / lung development / erythrocyte differentiation / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitochondrion organization / 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 / mRNA transcription 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 / multicellular organismal-level iron ion homeostasis / Regulation of expression of SLITs and ROBOs / transcription coactivator binding / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of cold-induced thermogenesis / Neddylation / microtubule cytoskeleton / regulation of gene expression / response to oxidative stress / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / angiogenesis / protein-macromolecule adaptor activity / transcription regulator complex / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / protein stabilization / nuclear speck / protein ubiquitination / cilium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / 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 / chromatin / positive regulation of DNA-templated transcription / enzyme binding / endoplasmic reticulum
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / 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 / Elongin C; Chain C, domain 1 / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / PAS repeat profile. / PAS domain / PAS domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsTarade, D. / Ohh, M. / Lee, J.E.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-77718 (M.O) Canada
Canadian Institutes of Health Research (CIHR)MOP-136978 (M.O) Canada
Canadian Institutes of Health Research (CIHR)MOP-133694 (J.E.L) Canada
CitationJournal: Nat Commun / Year: 2018
Title: HIF-2 alpha-pVHL complex reveals broad genotype-phenotype correlations in HIF-2 alpha-driven disease.
Authors: Tarade, D. / Robinson, C.M. / Lee, J.E. / Ohh, M.
History
DepositionDec 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: von Hippel-Lindau disease tumor suppressor
B: Elongin-B
C: Elongin-C
H: Hypoxia-Inducible Factor 2 alpha


Theoretical massNumber of molelcules
Total (without water)44,8914
Polymers44,8914
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, VHL-elongin B-elongin C (VBC) complex is supported by size exclusion chromatography. Biolayer interferometry kinetic binding experiments confirm binding of VBC complex to peptide substrate.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-47 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.770, 59.770, 246.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18702.291 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) / Strain (production host): BL21(DE3) / References: UniProt: P40337
#2: 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: 13147.781 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) / Strain (production host): BL21(DE3) / References: UniProt: Q15370
#3: 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: 10843.420 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) / Strain (production host): BL21(DE3) / References: UniProt: Q15369
#4: Protein/peptide Hypoxia-Inducible Factor 2 alpha


Mass: 2197.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.76 % / Description: Trapezoidal plates.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 26% (v/v) PEG-3350, 0.2 M Li2SO4, 0.1 M Bis-Tris. 7 mg/mL protein complex.
Temp details: Drops were set at 277 K. Incubated at 293 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.28339 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28339 Å / Relative weight: 1
ReflectionResolution: 2.002→48.307 Å / Num. obs: 31053 / % possible obs: 99.3 % / Redundancy: 8.54 % / CC1/2: 0.997 / Rrim(I) all: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 2.002→2.05 Å / Redundancy: 3.81 % / Mean I/σ(I) obs: 1.32 / Num. unique obs: 2084 / CC1/2: 0.701 / Rrim(I) all: 0.912 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LM8

1lm8


Resolution: 2.002→48.307 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.2355 1553 5 %
Rwork0.1986 --
obs0.2005 31047 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→48.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 0 102 2892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122861
X-RAY DIFFRACTIONf_angle_d1.0943900
X-RAY DIFFRACTIONf_dihedral_angle_d15.2711740
X-RAY DIFFRACTIONf_chiral_restr0.061451
X-RAY DIFFRACTIONf_plane_restr0.008505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.06660.34091290.29862452X-RAY DIFFRACTION93
2.0666-2.14050.25931380.2742612X-RAY DIFFRACTION99
2.1405-2.22620.31731400.23342658X-RAY DIFFRACTION100
2.2262-2.32750.24081370.21872607X-RAY DIFFRACTION100
2.3275-2.45020.23041390.20622657X-RAY DIFFRACTION100
2.4502-2.60370.25731420.21082686X-RAY DIFFRACTION100
2.6037-2.80470.26961410.2162670X-RAY DIFFRACTION100
2.8047-3.08690.24321410.22382688X-RAY DIFFRACTION100
3.0869-3.53350.26181440.21172746X-RAY DIFFRACTION100
3.5335-4.45130.20511460.15892760X-RAY DIFFRACTION100
4.4513-48.32150.20691560.17832958X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9293-1.47190.76627.1715-2.14456.43620.1005-0.22510.2325-0.3677-0.056-0.0288-0.18970.1846-0.09750.327-0.02270.05150.21610.03770.350445.261835.4697101.4883
24.7451-1.45492.32996.17590.61065.62230.26030.03280.2878-0.5152-0.1253-0.5433-0.1925-0.1209-0.08780.46350.01910.11540.23850.05750.372938.179342.300796.3569
34.98464.9377-1.30096.4817-4.74237.8391-0.02930.0593-0.7980.19150.4041.11740.2424-2.1822-0.50040.3114-0.03620.06890.62510.08920.599734.011430.2512108.3732
42.7646-1.1909-0.57611.08711.36132.27160.21380.31170.163-0.16-0.0460.05010.03810.0167-0.07270.3815-0.02910.00180.33170.00730.280248.392525.950196.4886
57.3566-1.9873-0.04584.27945.73229.05410.10790.08980.4637-0.1969-0.2369-0.1965-0.695-0.22510.08540.4054-0.06110.10630.2880.01950.404555.433736.1296104.4895
65.96222.61042.40646.44432.11753.5220.2447-0.06280.40380.1703-0.0015-0.2507-0.44890.3392-0.21360.3818-0.09440.00340.3634-0.07010.426460.038137.9958115.0659
72.4823-0.554-0.30052.44520.28053.50860.0364-0.16140.16980.04110.0784-0.17120.00490.2595-0.12830.2886-0.0598-0.00410.3167-0.0060.303152.066626.3474111.823
88.12442.80024.21259.60462.86536.9460.0365-0.1818-0.5149-0.46950.14161.2796-0.2047-0.43790.17260.45580.00470.10810.4860.08460.696825.124311.503139.2792
94.08220.3863-0.67431.69650.70764.011-0.0217-0.4041-0.27280.3528-0.04150.14920.369-0.35330.06520.4478-0.12570.02130.31360.04020.324635.959315.8134138.4821
106.3564-0.539-5.52273.17821.46067.75330.0121-0.25360.00460.31-0.10470.20030.0777-0.04880.05390.3789-0.14470.01440.3551-0.01820.340936.071419.5544136.3533
114.1469-2.2843-1.93132.48281.19614.36780.0229-0.2339-0.17320.1914-0.05740.03910.51520.4460.06890.4332-0.0526-0.05120.35610.0080.320150.472215.3931122.4778
123.43134.46222.63219.70810.10987.1459-0.65811.04020.7828-0.46280.96760.3052-0.22080.0614-0.40230.4001-0.0304-0.02750.62090.04970.461551.451223.1415140.2737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resid 1:18)
2X-RAY DIFFRACTION2(chain B and resid 19:62)
3X-RAY DIFFRACTION3(chain B and resid 63:68)
4X-RAY DIFFRACTION4(chain B and resid 69:106)
5X-RAY DIFFRACTION5(chain C and resid 17:34)
6X-RAY DIFFRACTION6(chain C and resid 35:57)
7X-RAY DIFFRACTION7(chain C and resid 58:112)
8X-RAY DIFFRACTION8(chain H and resid 527:540)
9X-RAY DIFFRACTION9(chain V and resid 59:105)
10X-RAY DIFFRACTION10(chain V and resid 106:141)
11X-RAY DIFFRACTION11(chain V and resid 142:193)
12X-RAY DIFFRACTION12(chain V and resid 194:209)

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