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- PDB-2juf: NMR solution structure of PARC CPH Domain. NESG Target HR3443B/SG... -

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Basic information

Entry
Database: PDB / ID: 2juf
TitleNMR solution structure of PARC CPH Domain. NESG Target HR3443B/SGC-Toronto
Componentsp53-associated parkin-like cytoplasmic protein
KeywordsGENE REGULATION / CPH domain / Structural Genomics Consortium / SGC / Northeast Structural Genomics Consortium / NESG / Alternative splicing / ATP-binding / Coiled coil / Cytoplasm / Metal-binding / Nucleotide-binding / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


cullin-RING ubiquitin ligase complex / regulation of mitotic nuclear division / microtubule cytoskeleton organization / ubiquitin protein ligase activity / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
: / : / : / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / IBR domain, a half RING-finger domain / IBR domain / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. ...: / : / : / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / IBR domain, a half RING-finger domain / IBR domain / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / SH3 type barrels. - #30 / Cullin, conserved site / Cullin family signature. / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / SH3 type barrels. / Armadillo-like helical / Armadillo-type fold / Ribosomal protein L2, domain 2 / Zinc finger, RING/FYVE/PHD-type / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsKaustov, L. / Liao, J.C.C. / Lemak, S. / Duan, S. / Muhandiram, R. / Karra, M. / Srisailam, S.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. ...Kaustov, L. / Liao, J.C.C. / Lemak, S. / Duan, S. / Muhandiram, R. / Karra, M. / Srisailam, S.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Dhe-Paganon, S. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of PARC CPH Domain.
Authors: Kaustov, L. / Liao, J.C.C. / Lemak, S. / Duan, S. / Muhandiram, R. / Karra, M. / Srisailam, S.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Dhe-Paganon, S. / Arrowsmith, C.H.
History
DepositionAug 23, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p53-associated parkin-like cytoplasmic protein


Theoretical massNumber of molelcules
Total (without water)11,6221
Polymers11,6221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein p53-associated parkin-like cytoplasmic protein / UbcH7-associated protein 1


Mass: 11621.732 Da / Num. of mol.: 1 / Fragment: CPH domain: Residues 366-466 / Mutation: S373G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARC, H7AP1, KIAA0708 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IWT3

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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 HN(CA)CB
1413D CBCA(CO)NH
1513D Cc(CO)NH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY
1913D HNCO
11013D HBHA(CO)NH
1111Hc(CO)NH-TOCSY

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Sample preparation

DetailsContents: 25 mM TRIS, 250 mM sodium chloride, 90 % H2O, 0.5 mM PMSF, 1 mM Benzamidine, 10 % D2O, 55 mM H2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMTRIS1
250 mMsodium chloride1
90 %H2O1
0.5 mMPMSF2
1 mMBenzamidine2
10 %D2O2
55 mMH2O2
Sample conditionsIonic strength: 0.25 / pH: 7.4 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
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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