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- PDB-6i7r: Structure of pVHL-elongin B-elongin C (VCB) in complex with hydro... -

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Basic information

Entry
Database: PDB / ID: 6i7r
TitleStructure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form
Components
  • Elongin-B
  • Elongin-C
  • Endothelial PAS domain-containing protein 1
  • von Hippel-Lindau disease tumor suppressor
KeywordsGENE REGULATION / E3 UBIQUITIN LIGASE / von Hippel Lindau / Prolyl hydroxylation / HIF / TUMOR SUPPRESSOR / CANCER / PROTEOSOMAL DEGRADATION / UBIQUITIN
Function / homology
Function and homology information


myoblast fate commitment / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / 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 / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / 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 / VCB complex / surfactant homeostasis / epithelial cell maturation / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Regulation of gene expression by Hypoxia-inducible Factor / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / 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 / ubiquitin-like ligase-substrate adaptor activity / embryonic placenta development / Tat-mediated elongation of the HIV-1 transcript / blood vessel remodeling / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / 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 / Pexophagy / regulation of heart rate / negative regulation of autophagy / transcription corepressor binding / erythrocyte differentiation / mitochondrion organization / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / lung development / mRNA transcription by RNA polymerase II / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / positive regulation of cold-induced thermogenesis / protein-macromolecule adaptor activity / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / angiogenesis / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / transcription regulator complex / amyloid fibril formation / molecular adaptor activity / response to hypoxia / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / nuclear speck / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II
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, 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, 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, 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 B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PAS domain / 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
FORMIC ACID / 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: 1.949 Å
AuthorsChowdhury, R. / Aguilera, L.S. / Schofield, C.J.
Citation
Journal: To Be Published
Title: HIF-2alpha-pVHL-elongin B-elongin C complex
Authors: Chowdhury, R. / Schofield, C.J.
#1: Journal: Nature / Year: 2002
Title: Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL.
Authors: Hon, W.C. / Wilson, M.I. / Harlos, K. / Claridge, T.D. / Schofield, C.J. / Pugh, C.W. / Maxwell, P.H. / Ratcliffe, P.J. / Stuart, D.I. / Jones, E.Y.
History
DepositionNov 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
B: Elongin-B
C: Elongin-C
H: Endothelial PAS domain-containing protein 1
V: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1375
Polymers45,0914
Non-polymers461
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-46 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.460, 61.460, 261.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 3 molecules BCV

#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: 13259.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Plasmid: PLASMID / Details (production host): pGEX-4T-3 / 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: 10957.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Plasmid: PLASMID / Details (production host): pBB75 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#4: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18558.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Plasmid: PLASMID / Details (production host): pGEX-4T-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337

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Protein/peptide , 1 types, 1 molecules H

#3: Protein/peptide Endothelial PAS domain-containing protein 1 / EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / ...EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / bHLHe73 / HIF-1-alpha-like factor / HLF / Hypoxia-inducible factor 2-alpha / HIF2-alpha / Member of PAS protein 2 / PAS domain-containing protein 2


Mass: 2315.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814

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Non-polymers , 2 types, 396 molecules

#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.8
Details: 0.1M Cacodyl-Na pH 5.8, 0.1M Mg Formate, 50mM Cystamine, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2017 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.949→262.01 Å / Num. obs: 38067 / % possible obs: 100 % / Redundancy: 24.9 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.035 / Rrim(I) all: 0.178 / Net I/σ(I): 14
Reflection shellResolution: 1.949→2.06 Å / Redundancy: 25.2 % / Rmerge(I) obs: 1.945 / Mean I/σ(I) obs: 2 / Num. unique obs: 5457 / CC1/2: 0.727 / Rpim(I) all: 0.393 / Rrim(I) all: 1.985 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LQB

1lqb


Resolution: 1.949→65.454 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.85
RfactorNum. reflection% reflection
Rfree0.203 1841 4.85 %
Rwork0.1731 --
obs0.1745 37921 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 52.7 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 1.949→65.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 3 395 3302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073036
X-RAY DIFFRACTIONf_angle_d1.0234136
X-RAY DIFFRACTIONf_dihedral_angle_d5.8812511
X-RAY DIFFRACTIONf_chiral_restr0.053463
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9486-2.00130.28931170.27182692X-RAY DIFFRACTION98
2.0013-2.06020.26061350.22852723X-RAY DIFFRACTION100
2.0602-2.12670.21171510.20782704X-RAY DIFFRACTION100
2.1267-2.20270.23571420.18642706X-RAY DIFFRACTION100
2.2027-2.29090.19131440.16982748X-RAY DIFFRACTION100
2.2909-2.39520.21231490.17912689X-RAY DIFFRACTION100
2.3952-2.52150.21261430.16782740X-RAY DIFFRACTION100
2.5215-2.67950.2221520.1722764X-RAY DIFFRACTION100
2.6795-2.88640.19631530.17122750X-RAY DIFFRACTION100
2.8864-3.17680.22911360.16432796X-RAY DIFFRACTION100
3.1768-3.63650.19491360.16172836X-RAY DIFFRACTION100
3.6365-4.58140.14331310.14252864X-RAY DIFFRACTION100
4.5814-65.49070.2171520.18743068X-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)
10.25270.4722-0.13020.4024-0.14990.2215-0.0589-0.09370.04770.1288-0.009-0.0957-0.1056-0.12870.00010.24940.0192-0.02960.2056-0.04530.216614.4856-23.9420.2097
20.72510.17010.02460.2087-0.12290.11790.1790.09770.522-0.3258-0.08040.3889-0.5636-0.3501-0.0660.59380.2-0.02970.3192-0.0620.4637-0.5378-8.766-10.0007
30.161-0.1232-0.10730.33380.03790.0616-0.2226-0.25160.1119-0.0674-0.27430.5408-0.0945-0.0242-0.00020.29540.1059-0.0380.3656-0.07580.3738-2.776-16.9977-6.2068
40.03560.0039-0.02260.04550.05160.04020.0192-0.1763-0.20640.1144-0.02330.55380.2836-0.67090.01160.3555-0.12560.0410.7510.07170.50023.6968-25.812114.3565
50.6825-0.1286-0.59080.3922-0.02360.7196-0.0604-0.0086-0.03490.0118-0.0663-0.09860.21240.0086-00.22120.01070.02510.2174-0.02170.223316.9133-46.9606-24.2148
60.07610.00080.10490.01810.04250.06550.0642-0.1370.1953-0.07970.1557-0.308-0.13380.5592-00.2886-0.00410.09230.3785-0.01470.369226.4604-43.4368-30.5817
70.1831-0.14960.07940.0707-0.08920.24220.0430.10290.0662-0.04580.0531-0.29350.10770.4490.00020.18740.00130.03040.3119-0.03440.239222.5128-39.1787-21.6236
80.5127-0.3911-0.05920.3875-0.49450.62440.03540.333-0.1478-0.1191-0.22450.2993-0.2039-0.049-0.03160.2866-0.00470.02770.24470.01030.15819.6668-31.3786-30.7824
90.34410.0941-0.20390.26820.01690.0805-0.03140.1344-0.2132-0.03560.00560.06260.1605-0.0987-0.00010.1771-0.0060.02770.2201-0.00430.23862.7265-41.8467-16.2279
100.0802-0.06260.11920.16-0.03510.116-0.03290.5948-0.4954-0.57310.1998-0.16570.0377-0.00620.0071-0.2603-0.1699-0.14620.3092-0.15911.0093-5.8381-51.4304-11.97
110.8510.0777-0.5310.68190.15720.34960.01950.0022-0.03850.09690.0392-0.0436-0.0474-0.03250.00010.1639-0.0070.01450.1885-0.00160.19846.7809-30.983-13.008
12-0.01370.0109-0.00390.0023-0.03740.1217-0.441-0.25710.27050.40070.33540.0656-0.12-0.22190.01020.53970.0187-0.01880.3449-0.17150.341420.0999-12.24929.187
130.0132-0.0005-0.03350.00080.00990.0188-0.16810.1680.15740.22330.0891-0.3365-0.0166-0.11340.00010.3621-0.024-0.03240.2438-0.03160.337131.4501-11.165616.8094
140.027-0.0447-0.01060.0469-0.04520.05440.10170.6987-0.23080.0005-0.3546-0.1007-0.12810.4878-0.00010.3303-0.02120.02330.4265-0.04130.489233.6006-18.12645.6862
150.17950.1475-0.08750.24440.03930.02220.1175-0.0485-0.00210.72670.15020.07260.0607-0.8320.01290.5036-0.11920.0450.54510.01660.256914.2755-19.692125.9683
160.53960.30620.79250.41110.1370.7698-0.00270.04510.03650.11010.0039-0.0948-0.0144-0.10770.01620.3025-0.0312-0.00950.1898-0.02520.234321.1127-17.898812.0125
170.29680.1207-0.13240.320.07680.3089-0.0061-0.08050.04140.14590.0311-0.03590.048-0.09690.00910.3452-0.037-0.04430.1888-0.00280.257416.5695-23.43389.7585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'V' and (resid 142 through 169 )
2X-RAY DIFFRACTION2chain 'V' and (resid 170 through 177 )
3X-RAY DIFFRACTION3chain 'V' and (resid 178 through 193 )
4X-RAY DIFFRACTION4chain 'V' and (resid 194 through 208 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 45 )
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 55 )
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 104 )
9X-RAY DIFFRACTION9chain 'C' and (resid 15 through 45 )
10X-RAY DIFFRACTION10chain 'C' and (resid 46 through 58 )
11X-RAY DIFFRACTION11chain 'C' and (resid 59 through 112 )
12X-RAY DIFFRACTION12chain 'H' and (resid 526 through 530 )
13X-RAY DIFFRACTION13chain 'H' and (resid 532 through 536 )
14X-RAY DIFFRACTION14chain 'H' and (resid 537 through 542 )
15X-RAY DIFFRACTION15chain 'V' and (resid 60 through 70 )
16X-RAY DIFFRACTION16chain 'V' and (resid 71 through 121 )
17X-RAY DIFFRACTION17chain 'V' and (resid 122 through 141 )

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