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- PDB-4b95: pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-... -

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Basic information

Entry
Database: PDB / ID: 4b95
TitlepVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide bound
Components
  • (TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ...) x 2
  • VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
KeywordsTRANSCRIPTION / HYPOXIA INDUCIBLE FACTOR / HIF-1ALPHA INHIBITOR
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, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / 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 ...von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / 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 / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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
ACETATE ION / Chem-UCK / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBuckley, D.L. / Gustafson, J.L. / VanMolle, I. / Roth, A.G. / SeopTae, H. / Gareiss, P.C. / Jorgensen, W.L. / Ciulli, A. / Crews, C.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Small-Molecule Inhibitors of the Interaction between the E3 Ligase Vhl and Hif1Alpha
Authors: Buckley, D.L. / Gustafson, J.L. / Van Molle, I. / Roth, A.G. / Tae, H.S. / Gareiss, P.C. / Jorgensen, W.L. / Ciulli, A. / Crews, C.M.
History
DepositionAug 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
B: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
C: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
D: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
E: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
F: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
G: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
H: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
I: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
J: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
K: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
L: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,93117
Polymers171,29912
Non-polymers1,6325
Water3,477193
1
A: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
B: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
C: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2775
Polymers42,8253
Non-polymers4522
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-40.7 kcal/mol
Surface area15230 Å2
MethodPISA
2
D: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
E: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
F: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2184
Polymers42,8253
Non-polymers3931
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-37.5 kcal/mol
Surface area15360 Å2
MethodPISA
3
G: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
H: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
I: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2184
Polymers42,8253
Non-polymers3931
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-40.7 kcal/mol
Surface area15460 Å2
MethodPISA
4
J: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
K: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
L: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2184
Polymers42,8253
Non-polymers3931
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-39.8 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.040, 93.040, 362.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 2 types, 8 molecules ADGJBEHK

#1: Protein
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 / ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / SIII P18


Mass: 13147.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370
#2: Protein
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 / ELONGIN 15 KDA SUBUNIT / ELONGIN-C / ELOC / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / SIII P15


Mass: 10974.616 Da / Num. of mol.: 4 / Fragment: RESIDUES 18-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369

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Protein , 1 types, 4 molecules CFIL

#3: Protein
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR / PROTEIN G7 / PVHL


Mass: 18702.291 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40337

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Non-polymers , 3 types, 198 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-UCK / (2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 393.264 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H18Cl2N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15 % PEG8000, 50MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97903
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. obs: 38647 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.71
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.97 / % possible all: 96.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
BUSTERTNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PVHL54-213-ELOB-ELOC APO STRUCTURE

Resolution: 2.8→27.59 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.342
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1960 5.08 %RANDOM
Rwork0.1847 ---
obs0.1873 38613 95.55 %-
Displacement parametersBiso mean: 57.68 Å2
Baniso -1Baniso -2Baniso -3
1-3.5479 Å20 Å20 Å2
2--3.5479 Å20 Å2
3----7.0957 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9894 0 108 193 10195
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110260HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2314016HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3305SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes199HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1513HARMONIC5
X-RAY DIFFRACTIONt_it10260HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion21.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1408SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11613SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2918 147 5.03 %
Rwork0.2039 2773 -
all0.2084 2920 -
obs--95.55 %
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)
14.8262-2.1442-0.95362.00791.54564.1268-0.0354-0.3988-0.25160.1457-0.0709-0.0790.29480.05050.1063-0.0236-0.04610.0778-0.07320.0955-0.2159-17.95082.639742.9632
23.22170.4545-2.85993.14320.55514.13930.0317-0.0006-0.2571-0.1798-0.175-0.24140.1594-0.03320.14330.1092-0.01760.1299-0.13750.0109-0.1543-14.5036-1.473725.8336
30.83580.48050.50087.1814-3.64263.93410.09440.13890.0165-0.2869-0.0362-0.029-0.0238-0.0864-0.05830.07170.00170.255-0.1878-0.0437-0.1962-7.502919.25558.9428
41.9465-2.2289-1.35234.21411.82495.38090.1121-0.71220.08090.449-0.04360.4820.7468-0.4204-0.06850.0065-0.13320.05940.02380.0286-0.281128.3426-1.232443.8461
52.35920.6279-2.80183.4861.03286.9258-0.0041-0.019-0.33110.0928-0.11950.02210.4415-0.42360.12360.0538-0.08920.066-0.13490.0172-0.17632.1884-5.290726.0554
61.4002-0.4557-0.57044.8175-0.95283.82620.1712-0.0094-0.0082-0.3273-0.05420.0691-0.3196-0.1044-0.11710.1146-0.01780.1129-0.1905-0.0302-0.20439.155714.37138.9643
72.0584-0.9432-0.57792.34860.35066.588-0.1989-0.30880.23750.35420.14830.33420.4821-0.39020.05060.1488-0.01170.1503-0.09760.0484-0.311632.928444.046543.404
81.2271.4683-1.14712.8550.35285.04670.00260.1110.19860.0031-0.03230.38970.7178-0.36110.02970.2513-0.03860.091-0.14180.0317-0.252934.720140.59525.5755
91.3696-0.65280.07463.3235-0.71581.4650.11380.0030.0927-0.4108-0.1629-0.0730.1874-0.06110.04920.317-0.0170.1267-0.17550.0111-0.291639.375161.60858.3231
103.3891-2.291-0.19332.6661.1985.761-0.0909-0.33060.25040.2491-0.0153-0.02510.6023-0.45150.10610.0634-0.11030.0926-0.09980.0327-0.276-14.468247.983743.0788
111.22122.2199-1.49344.71220.11785.85260.04160.1526-0.004-0.1474-0.11230.15690.6648-0.19990.07070.1625-0.06380.1258-0.13530.0178-0.1853-12.307644.903625.3383
121.41010.2451-0.33713.2093-0.91122.79430.0742-0.00860.0369-0.3358-0.1958-0.02150.058-0.00240.12160.16020.01460.2423-0.2111-0.0171-0.2024-7.240665.55698.1626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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