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- PDB-1v92: Solution structure of the UBA domain from p47, a major cofactor o... -

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Basic information

Entry
Database: PDB / ID: 1v92
TitleSolution structure of the UBA domain from p47, a major cofactor of the AAA ATPase p97
ComponentsNSFL1 cofactor p47
KeywordsRECOMBINATION / 3-helix bundle
Function / homology
Function and homology information


positive regulation of mitotic centrosome separation / negative regulation of protein localization to centrosome / RHOH GTPase cycle / nuclear membrane reassembly / Golgi stack / VCP-NSFL1C complex / spindle pole centrosome / Golgi organization / establishment of mitotic spindle orientation / autophagosome assembly ...positive regulation of mitotic centrosome separation / negative regulation of protein localization to centrosome / RHOH GTPase cycle / nuclear membrane reassembly / Golgi stack / VCP-NSFL1C complex / spindle pole centrosome / Golgi organization / establishment of mitotic spindle orientation / autophagosome assembly / ubiquitin binding / chromosome / ATPase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane fusion / lipid binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain ...SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Ubiquitin-associated (UBA) domain / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsYuan, X. / Simpson, P. / Mckeown, C. / Kondo, H. / Uchiyama, K. / Wallis, R. / Dreveny, I. / Keetch, C. / Zhang, X. / Robinson, C. ...Yuan, X. / Simpson, P. / Mckeown, C. / Kondo, H. / Uchiyama, K. / Wallis, R. / Dreveny, I. / Keetch, C. / Zhang, X. / Robinson, C. / Freemont, P. / Matthews, S.
CitationJournal: Embo J. / Year: 2004
Title: Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97
Authors: Yuan, X. / Simpson, P. / McKeown, C. / Kondo, H. / Uchiyama, K. / Wallis, R. / Dreveny, I. / Keetch, C. / Zhang, X. / Robinson, C. / Freemont, P. / Matthews, S.
History
DepositionJan 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4Dec 27, 2023Group: 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: NSFL1 cofactor p47


Theoretical massNumber of molelcules
Total (without water)5,1731
Polymers5,1731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide NSFL1 cofactor p47 / p97 cofactor p47 / XY body-associated protein XY40


Mass: 5172.608 Da / Num. of mol.: 1 / Fragment: p47 UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pPRO-EX HTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 DE3 / References: UniProt: O35987

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
115N, 13C double labelled p47 residues 1-17420mM sodium acetate
215N labelled p47 residues 1-17420mM sodium acetate
Sample conditionsIonic strength: 20mM NaAc / pH: 5.3 / Pressure: 1 atm / Temperature: 298 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 DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1F.Delaglioprocessing
XwinNMR1Burkercollection
NMRView4.0.3B.Johnsondata analysis
ARIA1M.Nilges, J.P.Lingestructure solution
ARIA1M.Nilges, J.P.Lingerefinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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