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- PDB-4awj: pVHL:EloB:EloC complex, in complex with capped Hydroxyproline -

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Basic information

Entry
Database: PDB / ID: 4awj
TitlepVHL:EloB:EloC complex, in complex with capped Hydroxyproline
Components
  • (TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ...) x 2
  • VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
KeywordsTRANSCRIPTION / E3 UBIQUITIN LIGASE / TUMOR SUPRESSOR
Function / homology
Function and homology information


regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle ...regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / 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 / 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 / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / 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 / 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 / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / Neddylation / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / protein-macromolecule adaptor activity / amyloid fibril formation / DNA-binding transcription factor binding / ubiquitin-dependent protein catabolic process / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cilium / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ 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
ACETATE ION / ACETIC ACID / (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsVan Molle, I. / Thomann, A. / Buckley, D.L. / So, E.C. / Lang, S. / Crews, C.M. / Ciulli, A.
CitationJournal: Chem.Biol. / Year: 2012
Title: Dissecting Fragment-Based Lead Discovery at the Von Hippel-Lindau Protein:Hypoxia Inducible Factor 1Alpha Protein-Protein Interface.
Authors: Van Molle, I. / Thomann, A. / Buckley, D.L. / So, E.C. / Lang, S. / Crews, C.M. / Ciulli, A.
History
DepositionJun 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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)168,75324
Polymers167,50212
Non-polymers1,25112
Water5,206289
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)42,2397
Polymers41,8753
Non-polymers3634
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-38.7 kcal/mol
Surface area15490 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)42,1816
Polymers41,8753
Non-polymers3053
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-32.2 kcal/mol
Surface area15840 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)42,1215
Polymers41,8753
Non-polymers2452
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-40.4 kcal/mol
Surface area16260 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)42,2136
Polymers41,8753
Non-polymers3373
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-40.7 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.400, 93.400, 362.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

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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: 11956.372 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-104
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 17-112
Source method: isolated from a genetically manipulated source
Details: EXTRA M AT N-TERMINUS AS RESULT OF CLONING / 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: 18944.420 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 , 5 types, 301 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-V6F / (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide


Mass: 186.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14N2O3
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (V6F): CAPPED HYDROXYPROLINE
Sequence detailsGSH REMAINING AFTER THROMBIN CLEAVAGE EXTRA M AT N-TERMINUS AS RESULT OF 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: 2.38 Å3/Da / Density % sol: 48.31 % / Description: NONE
Crystal growpH: 6
Details: 0.1 M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 28, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 56728 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 12.6 % / Biso Wilson estimate: 46.53 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.34
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.25 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→29.536 Å / SU ML: 0.41 / σ(F): 2.01 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 2834 5 %
Rwork0.2202 --
obs0.2224 56672 99.89 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.169 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.6276 Å20 Å20 Å2
2--13.6276 Å20 Å2
3---4.2148 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10389 0 86 289 10764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210721
X-RAY DIFFRACTIONf_angle_d0.63414573
X-RAY DIFFRACTIONf_dihedral_angle_d12.6043971
X-RAY DIFFRACTIONf_chiral_restr0.0441666
X-RAY DIFFRACTIONf_plane_restr0.0031888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.37181390.32182640X-RAY DIFFRACTION100
2.5431-2.58930.42161400.30962645X-RAY DIFFRACTION100
2.5893-2.63910.37921380.2972628X-RAY DIFFRACTION100
2.6391-2.69290.32811390.2812648X-RAY DIFFRACTION100
2.6929-2.75140.33331420.26022685X-RAY DIFFRACTION100
2.7514-2.81540.28251370.25252611X-RAY DIFFRACTION100
2.8154-2.88570.34191390.25162645X-RAY DIFFRACTION100
2.8857-2.96370.30661390.23712630X-RAY DIFFRACTION100
2.9637-3.05080.30821410.2432674X-RAY DIFFRACTION100
3.0508-3.14920.27731400.24362673X-RAY DIFFRACTION100
3.1492-3.26160.26861410.23282670X-RAY DIFFRACTION100
3.2616-3.3920.32931400.23612659X-RAY DIFFRACTION100
3.392-3.54610.26531410.23032688X-RAY DIFFRACTION100
3.5461-3.73270.27481420.2242706X-RAY DIFFRACTION100
3.7327-3.96610.22631410.20842679X-RAY DIFFRACTION100
3.9661-4.27150.23231440.18472730X-RAY DIFFRACTION100
4.2715-4.69980.20161430.16252725X-RAY DIFFRACTION100
4.6998-5.37630.22191450.18482748X-RAY DIFFRACTION100
5.3763-6.76020.26461480.23762807X-RAY DIFFRACTION100
6.7602-29.53770.22051550.20542947X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.7793 Å / Origin y: 30.0951 Å / Origin z: 23.9475 Å
111213212223313233
T0.2767 Å2-0.0455 Å20.1282 Å2--0.2 Å20.1153 Å2--0.0383 Å2
L0.0427 °2-0.0096 °20.0549 °2-0.1008 °20.002 °2---0.0299 °2
S0.004 Å °-0.004 Å °-0.0083 Å °-0.0796 Å °-0.0517 Å °0.0263 Å °0.0128 Å °-0.036 Å °0.0051 Å °
Refinement TLS groupSelection details: ALL

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