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- PDB-1i42: NMR STRUCTURE OF THE UBX DOMAIN FROM P47 -

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Basic information

Entry
Database: PDB / ID: 1i42
TitleNMR STRUCTURE OF THE UBX DOMAIN FROM P47
ComponentsP47
KeywordsPROTEIN BINDING / Ubiquitin superfold / UBX / unusual N-terminal feature
Function / homology
Function and homology information


negative regulation of protein localization to centrosome / RHOH GTPase cycle / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / Golgi stack / VCP-NSFL1C complex / spindle pole centrosome / Golgi organization / establishment of mitotic spindle orientation / autophagosome assembly ...negative regulation of protein localization to centrosome / RHOH GTPase cycle / positive regulation of mitotic centrosome separation / 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 / 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
AuthorsYuan, X. / Shaw, A. / Zhang, X. / Kondo, H. / Lally, J. / Freemont, P.S. / Matthews, S.
CitationJournal: 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.
History
DepositionFeb 19, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 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 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: P47


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)10 / 100back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein P47


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, HN(CO)CA, CBCA(CO)NH, HBHA(CO)NH, 15N-NOESY
222IPAP-HSQC
3332D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 13C, 15N-labelled p47 C domain sample20mM NaAc buffer pH5.2; 90% H2O, 10% D2O
21mM 15N p47 C domain sample3% C12E5/hexanol (r=0.96)
31mM p47 C domain sample99.9% D2O, pH5.2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.2 1 atm302 K
25.2 1 atm302 K
35.2 1 atm302 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AURELIA2.1.5processing
NMRPipeFrank Delaglioprocessing
X-PLOR3.853A. Brungerstructure solution
NMRView3.1.1Bruce Johnsondata analysis
XwinNMRprocessing
X-PLOR3.853A. Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the ...Conformer selection criteria: back calculated data agree with experimental NOESY spectrum,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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