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- PDB-1jru: NMR STRUCTURE OF THE UBX DOMAIN FROM P47 (ENERGY MINIMISED AVERAGE) -

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Basic information

Entry
Database: PDB / ID: 1jru
TitleNMR STRUCTURE OF THE UBX DOMAIN FROM P47 (ENERGY MINIMISED AVERAGE)
Componentsp47 protein
KeywordsUNKNOWN FUNCTION / UBIQUITIN SUPERFOLD / UBX / UNUSUAL N-TERMINAL FEATURE
Function / homology
Function and homology information


RHOH GTPase cycle / negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / spindle pole centrosome / VCP-NSFL1C complex / Golgi stack / Golgi organization / establishment of mitotic spindle orientation / autophagosome assembly ...RHOH GTPase cycle / negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / spindle pole centrosome / VCP-NSFL1C complex / Golgi stack / 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 / cytoplasm / cytosol
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 / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model type detailsminimized average
AuthorsYuan, X.M. / Shaw, A. / Zhang, X.D. / Kondo, H. / Lally, J. / Freemont, P.S. / Matthews, S.J.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution structure and interaction surface of the C-terminal domain from p47: a major p97-cofactor involved in SNARE disassembly.
Authors: Yuan, X. / Shaw, A. / Zhang, X. / Kondo, H. / Lally, J. / Freemont, P.S. / Matthews, S.
#1: Journal: Nature / Year: 1997
Title: p47 is a cofactor for p97-mediated membrane fusion
Authors: Kondo, H. / Rabouille, C. / Newman, R. / Levine, T.P. / Pappin, D. / Freemont, P.S. / Warren, G.
History
DepositionAug 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 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

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Assembly

Deposited unit
A: p47 protein


Theoretical massNumber of molelcules
Total (without water)9,9011
Polymers9,9011
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein p47 protein / XY40 protein


Mass: 9901.343 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RESIDUES 282-370)
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
111HNCA
121HN(CO)CA
131HN(CA)CB
141CBCA(CO)NH
151HBHA(CBCACO)NH
1613D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1mM 13C, 15N-labelled p47 C-terminal domain sample in 20 mM NaAc, pH5.2
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.2 / Pressure: 1 atm / Temperature: 302 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AURELIA2.1.5Brukerdata analysis
NMRPipeDelaglioprocessing
XwinNMRBrukercollection
NMRView3.1.1Johnsondata analysis
X-PLOR3.853Brungerstructure solution
X-PLOR3.853Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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