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- PDB-6fmi: pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-... -

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Basic information

Entry
Database: PDB / ID: 6fmi
TitlepVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-oxopropan-2-yl)acetamide (ligand 2)
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / protein complex / ubiquitin ligase / hypoxia inducible factor
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
Chem-DV2 / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSoares, P. / Lucas, X. / Ciulli, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460 DrugE3CRLs United Kingdom
CitationJournal: Bioorg. Med. Chem. / Year: 2018
Title: Thioamide substitution to probe the hydroxyproline recognition of VHL ligands.
Authors: Soares, P. / Lucas, X. / Ciulli, A.
History
DepositionJan 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2318
Polymers81,3386
Non-polymers8932
Water2,252125
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1164
Polymers40,6693
Non-polymers4471
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-38 kcal/mol
Surface area16870 Å2
MethodPISA
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1164
Polymers40,6693
Non-polymers4471
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-41 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.972, 69.863, 356.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

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Components

#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: 11956.372 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / 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: 10974.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 17738.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#4: Chemical ChemComp-DV2 / ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]ethanamide


Mass: 446.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26N4O3S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 49.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, MgOAc, Sodium cacodylate, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.8→47.18 Å / Num. obs: 20290 / % possible obs: 99.9 % / Redundancy: 5 % / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
Aimless0.5.9data scaling
PDB_EXTRACT3.22data extraction
RefinementResolution: 2.8→47.18 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / SU B: 32.044 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25641 1040 5.1 %RANDOM
Rwork0.19827 ---
obs0.2012 19194 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20 Å2
2---0.36 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5317 0 60 125 5502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195501
X-RAY DIFFRACTIONr_bond_other_d0.0020.025289
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9987471
X-RAY DIFFRACTIONr_angle_other_deg0.8643.00312172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2723.307254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27115925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7141548
X-RAY DIFFRACTIONr_chiral_restr0.0630.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021234
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6043.9122638
X-RAY DIFFRACTIONr_mcbond_other1.6043.9112637
X-RAY DIFFRACTIONr_mcangle_it2.6786.5793280
X-RAY DIFFRACTIONr_mcangle_other2.6776.5813281
X-RAY DIFFRACTIONr_scbond_it2.0324.2212863
X-RAY DIFFRACTIONr_scbond_other2.0314.2222864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2976.9924192
X-RAY DIFFRACTIONr_long_range_B_refined5.32817.4795699
X-RAY DIFFRACTIONr_long_range_B_other5.32817.4825700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 79 -
Rwork0.287 1345 -
obs--99.72 %
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)
12.9056-0.26091.63821.2807-0.12673.81720.22730.9365-0.0228-0.3175-0.1837-0.0065-0.10060.5141-0.04360.1643-0.00010.02180.6816-0.03610.006818.1981.462351.031
22.88391.94381.22692.0062-0.67714.4372-0.17430.41790.0131-0.05860.1658-0.0806-0.08660.38660.00850.1058-0.1718-0.01780.4996-0.01360.072223.29483.214368.419
33.89531.2654-1.38172.3054-0.4942.1438-0.10870.2404-0.0839-0.05290.0651-0.08370.0154-0.09920.04360.2284-0.1431-0.08220.33540.01950.038813.87163.838385.548
42.19940.33370.76145.4014-2.44274.58760.0584-0.49850.0091-0.0195-0.422-0.41580.10810.51520.36360.4658-0.0278-0.08950.88550.0220.062711.3694.031437.312
55.3682.02650.36823.3103-1.66853.3551-0.57820.15780.1561-0.1850.168-0.07770.27760.44470.41020.4692-0.1599-0.0720.69030.01420.127712.06999.314419.896
63.11211.00120.98914.68511.00312.6695-0.23560.44720.1141-0.69550.12630.1007-0.25520.20460.10930.2514-0.1504-0.0580.45050.07060.0186-6.70588.29403.111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2B17 - 112
3X-RAY DIFFRACTION3C62 - 202
4X-RAY DIFFRACTION4D1 - 103
5X-RAY DIFFRACTION5E17 - 112
6X-RAY DIFFRACTION6F62 - 202

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