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- PDB-3ztd: pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-... -

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Basic information

Entry
Database: PDB / ID: 3ztd
TitlepVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate
Components
  • TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
  • TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
  • VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
KeywordsTRANSCRIPTION / TUMOUR SUPRESSOR PROTEIN / PVHL E3 UBIQUITIN LIGASE
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 / Replication of the SARS-CoV-1 genome / VCB complex / 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 / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / 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 / 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 / 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 / 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 / molecular adaptor activity / cellular response to hypoxia / DNA-binding transcription factor binding / 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 / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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 / 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
Chem-ZTD / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsVanMolle, I. / Buckley, D.L. / 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
DepositionJul 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Structure summary
Revision 1.2Dec 20, 2023Group: 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

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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)172,90416
Polymers171,29912
Non-polymers1,6064
Water23413
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)43,2264
Polymers42,8253
Non-polymers4011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-35.2 kcal/mol
Surface area16050 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)43,2264
Polymers42,8253
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-36.6 kcal/mol
Surface area16360 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)43,2264
Polymers42,8253
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-36 kcal/mol
Surface area16290 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)43,2264
Polymers42,8253
Non-polymers4011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-39.5 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.081, 94.081, 366.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#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 / ELONGINB


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 / ...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
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
#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
#4: Chemical
ChemComp-ZTD / METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE


Mass: 401.413 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23N3O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsP40337 EXTENDED WITH G52 AND S53 ARE FROM AN EXPRESSION TAG. Q15369 RES 17-112 EXTRA M AT C- ...P40337 EXTENDED WITH G52 AND S53 ARE FROM AN EXPRESSION TAG. Q15369 RES 17-112 EXTRA M AT C-TERMINUS FROM CLONING. P40337 ISOFORM 1 USED.

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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: 2.78 Å3/Da / Density % sol: 55.45 % / Description: NONE
Crystal growDetails: 0.1 M NA CITRATE PH 5.7, 0.2 M MG ACETATE, 15% PEG8000, 50 MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2010
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 42297 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 14.2 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.78
Reflection shellResolution: 2.79→2.96 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.71 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZRF

3zrf


Resolution: 2.79→47.04 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.872 / SU B: 17.05 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.30898 2115 5 %RANDOM
Rwork0.22443 ---
obs0.22866 40180 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.79→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10279 0 116 13 10408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02210638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2031.99214476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53451301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81223.568454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.099151704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3811573
X-RAY DIFFRACTIONr_chiral_restr0.1310.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0228099
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.91.56655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.734210779
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.53133983
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2124.53697
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.79→2.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 151 -
Rwork0.256 2871 -
obs--100 %

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