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- PDB-4bks: von Hippel Lindau protein:ElonginB:ElonginC complex, in complex w... -

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Basic information

Entry
Database: PDB / ID: 4bks
Titlevon Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
Components
  • (TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ...) x 3
  • VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
KeywordsPROTEIN TRANSPORT / E3 UBIQUITIN LIGASE / FRAGMENT BASED DRUG DISCOVERY
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / 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 / Tat-mediated elongation of the HIV-1 transcript / 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 / negative regulation of autophagy / transcription corepressor binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription factor binding / amyloid fibril formation / protein stabilization / molecular adaptor activity / protein ubiquitination / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 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 / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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-X6C / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsVan Molle, I. / Dias, D.M. / Baud, M. / Galdeano, C. / Geraldes, C.F.G.C. / Ciulli, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions?
Authors: Dias, D.M. / Van Molle, I. / Baud, M.G.J. / Galdeano, C. / Geraldes, C.F.G.C. / Ciulli, A.
History
DepositionApr 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references

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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)167,76118
Polymers166,32512
Non-polymers1,4356
Water10,881604
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)42,0225
Polymers41,6333
Non-polymers3882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-41.3 kcal/mol
Surface area15650 Å2
MethodPISA
2
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)42,0225
Polymers41,6333
Non-polymers3882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-40.4 kcal/mol
Surface area16420 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)41,8594
Polymers41,5293
Non-polymers3291
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-39.2 kcal/mol
Surface area16090 Å2
MethodPISA
4
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)41,8594
Polymers41,5293
Non-polymers3291
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-34.8 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.590, 93.590, 363.740
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 ... , 3 types, 8 molecules AJBEHKDG

#1: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 / ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / ...ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / SIII P18 / ELONGINB1-104


Mass: 11852.389 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF_DUET1 / 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 / ...ELONGIN 15 KDA SUBUNIT / ELONGIN-C / ELOC / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / SIII P15 / ELONGINC


Mass: 10974.616 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF_DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369
#4: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 / ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / ...ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / SIII P18 / ELONGINB1-104


Mass: 11748.406 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF_DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370

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Protein , 1 types, 4 molecules CFIL

#3: Protein
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR / PROTEIN G7 / PVHL / PVHL54-213


Mass: 18806.273 Da / Num. of mol.: 4 / Fragment: RESIDUES 214-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40337

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Non-polymers , 3 types, 610 molecules

#5: Chemical
ChemComp-X6C / (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 329.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H19N3O4
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsO74: THE LIGAND 6-(4-(2-CHLOROANILINO)-1H-QUINAZOLIN-2-YLIDENE) CYCLOHEXA-2, 4-DIEN-1-ONE IS BOUND ...O74: THE LIGAND 6-(4-(2-CHLOROANILINO)-1H-QUINAZOLIN-2-YLIDENE) CYCLOHEXA-2, 4-DIEN-1-ONE IS BOUND AT THE INTERFACES BETWEEN PROTEIN CHAINS A AND B AND BETWEEN PROTEIN CHAINS C AND D.
Sequence detailsGS LEFT FROM CLEAVABLE TAG 2 MET AT N-TERMINUS DUE TO CLONING

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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: 2.32 Å3/Da / Density % sol: 46.91 % / Description: NONE
Crystal growDetails: 0.1M NA CACODYALATE PH 6.0, 0.2M MG ACETATE, 15%PEG3350, 5MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 83354 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 12.9 % / Biso Wilson estimate: 46.23 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.95
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.18 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
BUSTERTNTphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→45.47 Å / Cor.coef. Fo:Fc: 0.9529 / Cor.coef. Fo:Fc free: 0.9396 / SU R Cruickshank DPI: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.231 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.181
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11117. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=48. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11117. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=48. NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 4160 4.99 %RANDOM
Rwork0.1876 ---
obs0.1895 83334 99.98 %-
Displacement parametersBiso mean: 57.69 Å2
Baniso -1Baniso -2Baniso -3
1--4.3523 Å20 Å20 Å2
2---4.3523 Å20 Å2
3---8.7046 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 104 604 11132
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110815HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1714721HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3632SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes239HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1569HARMONIC5
X-RAY DIFFRACTIONt_it10815HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion19.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1433SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12012SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2292 296 4.92 %
Rwork0.2142 5723 -
all0.215 6019 -
obs--99.98 %
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)
13.6518-1.4069-1.81292.37771.43213.8735-0.1884-0.2898-0.14490.18640.05950.01780.25460.15480.1289-0.1113-0.0180.0494-0.14420.0249-0.1592-17.79042.381343.2626
21.5876-0.1049-1.18943.92130.36694.11990.00840.0997-0.1853-0.362-0.08090.0864-0.0044-0.05730.0725-0.04690.00610.0369-0.1527-0.0085-0.1543-14.5956-1.747126.0593
30.8676-0.294-0.00645.2332-2.44262.7510.0670.02610.0192-0.2968-0.01140.1535-0.17270.0095-0.05560.173-0.05430.1828-0.2312-0.0422-0.2052-7.697319.20118.9426
43.1314-1.5069-1.89863.03053.23786.8532-0.1102-0.4419-0.07080.7039-0.00970.39781.3437-0.31640.120.147-0.13010.0524-0.16940.0285-0.34128.8789-1.598744.019
50.97140.2659-1.40615.47921.7096.4108-0.00470.0658-0.15610.5011-0.07650.15260.6851-0.29140.08120.1131-0.0671-0.0084-0.20710.0054-0.253932.5914-5.844726.1497
61.3873-0.6880.10555.5849-1.43193.36250.23770.14-0.0059-0.3831-0.037-0.0656-0.5833-0.0336-0.20080.1766-0.01290.1411-0.2616-0.0442-0.248139.361614.02348.9342
71.9454-1.235-1.28383.17660.29144.9452-0.0824-0.05890.00940.27830.00210.33230.1172-0.40320.0803-0.0291-0.01940.0869-0.16430.042-0.197433.802143.750143.6894
81.12390.4696-0.83123.698-0.44933.1025-0.00920.1168-0.0958-0.6337-0.0730.46980.4603-0.44930.08220.1645-0.0053-0.012-0.1930.0353-0.219635.610640.21325.771
91.4108-0.48490.2052.6676-1.05782.3081-0.0861-0.0042-0.0215-0.285-0.06210.03850.34440.03330.14820.17080.01260.0181-0.2463-0.0059-0.252139.790561.42828.4492
102.6295-0.7553-0.67022.0028-0.16582.9395-0.0126-0.14790.05020.1304-0.05710.00960.1465-0.04230.0697-0.1046-0.04180.0377-0.09030.013-0.161-14.032347.813443.3055
111.16820.7265-0.81882.9318-0.83113.3972-0.04190.036-0.0612-0.4343-0.0920.04440.4708-0.10250.13380.0454-0.02630.0399-0.15070.0199-0.1708-11.84545.002525.5584
121.3865-0.23360.10272.8953-1.32692.5328-0.012-0.0027-0.0255-0.4813-0.10280.08080.31540.02220.11490.0479-0.00220.0937-0.2254-0.0262-0.2022-7.208565.69558.2328
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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