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- PDB-1hv2: SOLUTION STRUCTURE OF YEAST ELONGIN C IN COMPLEX WITH A VON HIPPE... -

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Basic information

Entry
Database: PDB / ID: 1hv2
TitleSOLUTION STRUCTURE OF YEAST ELONGIN C IN COMPLEX WITH A VON HIPPEL-LINDAU PEPTIDE
Components
  • ELONGIN C
  • VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
KeywordsSIGNALING PROTEIN / protein-peptide complex
Function / homology
Function and homology information


regulation of catecholamine metabolic process / RHOBTB3 ATPase cycle / nucleotide-excision repair factor 4 complex / homeostasis of number of retina cells / pancreatic A cell differentiation / SUMOylation of ubiquitinylation proteins / regulation of thymocyte apoptotic process / ciliary body morphogenesis / type B pancreatic cell differentiation / iris morphogenesis ...regulation of catecholamine metabolic process / RHOBTB3 ATPase cycle / nucleotide-excision repair factor 4 complex / homeostasis of number of retina cells / pancreatic A cell differentiation / SUMOylation of ubiquitinylation proteins / regulation of thymocyte apoptotic process / ciliary body morphogenesis / type B pancreatic cell differentiation / iris morphogenesis / negative regulation of endothelial cell differentiation / hypoxia-inducible factor-1alpha signaling pathway / melanin metabolic process / eye pigmentation / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / blood vessel endothelial cell migration / global genome nucleotide-excision repair / endothelial cell differentiation / regulation protein catabolic process at postsynapse / camera-type eye morphogenesis / Neddylation / regulation of apoptotic signaling pathway / elongin complex / negative regulation of thymocyte apoptotic process / Antigen processing: Ubiquitination & Proteasome degradation / regulation of postsynapse organization / VCB complex / Cul2-RING ubiquitin ligase complex / TP53 Regulates Transcription of DNA Repair Genes / Cul3-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-like ligase-substrate adaptor activity / response to UV / proteasomal protein catabolic process / negative regulation of TORC1 signaling / extracellular matrix organization / positive regulation of epithelial cell proliferation / nucleotide-excision repair / protein catabolic process / neuron differentiation / protein transport / regulation of protein localization / regulation of gene expression / ubiquitin-dependent protein catabolic process / response to ethanol / angiogenesis / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynaptic density / protein ubiquitination / cilium / negative regulation of gene expression / protein-containing complex binding / nucleolus / glutamatergic synapse / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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 / Potassium Channel Kv1.1; Chain A ...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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
von Hippel-Lindau disease tumor suppressor / Elongin-C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulating annealing
AuthorsBotuyan, M.V. / Mer, G. / Yi, G.-S. / Koth, C.M. / Case, D.A. / Edwards, A.M. / Chazin, W.J. / Arrowsmith, C.H.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution structure and dynamics of yeast elongin C in complex with a von Hippel-Lindau peptide.
Authors: Botuyan, M.V. / Mer, G. / Yi, G.S. / Koth, C.M. / Case, D.A. / Edwards, A.M. / Chazin, W.J. / Arrowsmith, C.H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Binding of Elongin A or a von Hippel-Lindau Peptide Stabilizes the Structure of Yeast Elongin C
Authors: Botuyan, M.V. / Koth, C.M. / Mer, G. / Chakrabartty, A. / Conaway, J.W. / Conaway, R.C. / Edwards, A.M. / Arrowsmith, C.H. / Chazin, W.J.
History
DepositionJan 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELONGIN C
B: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR


Theoretical massNumber of molelcules
Total (without water)13,1152
Polymers13,1152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100The submitted conformer models are the 20 structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ELONGIN C / ELC1


Mass: 11338.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q03071
#2: Protein/peptide VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR / G7 PROTEIN


Mass: 1776.195 Da / Num. of mol.: 1 / Fragment: RESIDUES 157-171 / Source method: obtained synthetically / Details: This peptide was chemically synthesized / References: UniProt: P40338

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY
1413D 13C/15N-filter-edited NOESY
1523D 13C/15N-filter-edited NOESY
1622D double-half filtered NOESY
1722D double-half filtered COSY
1822D double-half filtered TOCSY
191HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15; U-15N,13C; 10mM sodium phosphate buffer (pH 7.0); 100 mM NaCl; 7.5 mM DTT93% H2O/7% D2O
2U-15; U-15N,13C; 10mM sodium phosphate buffer (pH 7.0); 100 mM NaCl; 7.5 mM DTT100% D2O
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503
Bruker DRXBrukerDRX8004
Varian UNITYVarianUNITY5005
Varian UNITYPLUSVarianUNITYPLUS6006

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio et al.processing
DIANA2.8Guntert and Wuthrichstructure solution
Amber6Case et al.refinement
NMRView3Johnson and Blevinsdata analysis
RefinementMethod: distance geometry, simulating annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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