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- PDB-2jng: Solution structure of the CUL7-CPH domain from Homo Sapiens; Nort... -

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Basic information

Entry
Database: PDB / ID: 2jng
TitleSolution structure of the CUL7-CPH domain from Homo Sapiens; Northeast Structural Genomics Consortium target HT1.
ComponentsCullin-7
KeywordsGENE REGULATION / p53 binding domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


3M complex / anaphase-promoting complex / XBP1(S) activates chaperone genes / Cul7-RING ubiquitin ligase complex / positive regulation of dendrite morphogenesis / regulation of mitotic nuclear division / Golgi organization / mitotic cytokinesis / epithelial to mesenchymal transition / vasculogenesis ...3M complex / anaphase-promoting complex / XBP1(S) activates chaperone genes / Cul7-RING ubiquitin ligase complex / positive regulation of dendrite morphogenesis / regulation of mitotic nuclear division / Golgi organization / mitotic cytokinesis / epithelial to mesenchymal transition / vasculogenesis / placenta development / microtubule cytoskeleton organization / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / centrosome / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / proteolysis / cytosol / cytoplasm
Similarity search - Function
CPH domain / Mouse development and cellular proliferation protein Cullin-7 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / SH3 type barrels. - #30 / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain ...CPH domain / Mouse development and cellular proliferation protein Cullin-7 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / SH3 type barrels. - #30 / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Galactose-binding-like domain superfamily / SH3 type barrels. / Armadillo-type fold / Ribosomal protein L2, domain 2 / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsLemak, A. / Kaustov, L. / Lukin, J. / Duan, S. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Conserved CPH Domains of Cul7 and PARC Are Protein-Protein Interaction Modules That Bind the Tetramerization Domain of p53
Authors: Kaustov, L. / Lukin, J. / Lemak, A. / Duan, S. / Ho, M. / Doherty, R. / Penn, L.Z. / Arrowsmith, C.H.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cullin-7


Theoretical massNumber of molelcules
Total (without water)12,0131
Polymers12,0131
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cullin-7 / CUL-7


Mass: 12013.217 Da / Num. of mol.: 1 / Fragment: sequence database residues 360-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL7, KIAA0076 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14999

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D H(CCO)NH
NMR detailsText: The structure was determined using a combination of NOE and HN residual dipolar coupling data.

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Sample preparation

DetailsContents: 25 mM TRIS, 250 mM sodium chloride, 55 mM H2O, 0.5 mM PMSF, 0.5 mM TCEP, 1 mM Benzamidine, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMTRIS1
250 mMsodium chloride1
55 mMH2O1
0.5 mMPMSF1
0.5 mMTCEP1
1 mMBenzamidine1
Sample conditionsIonic strength: 250 / pH: 7.4 / Pressure: ambient / Temperature: 298.15 K

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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 AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.106Goddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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