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- PDB-1ss6: Solution structure of SEP domain from human p47 -

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Basic information

Entry
Database: PDB / ID: 1ss6
TitleSolution structure of SEP domain from human p47
ComponentsNSFL1 cofactor p47
KeywordsSIGNALING PROTEIN / NMR / p47 / SEP
Function / homology
Function and homology information


negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / Golgi stack / VCP-NSFL1C complex / Golgi organization / establishment of mitotic spindle orientation / RHOH GTPase cycle / autophagosome assembly / ubiquitin binding ...negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / Golgi stack / VCP-NSFL1C complex / Golgi organization / establishment of mitotic spindle orientation / RHOH GTPase cycle / autophagosome assembly / ubiquitin binding / chromosome / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane fusion / centrosome / lipid binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SEP 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. ...SEP 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 / Nucleotidyltransferase; domain 5 / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsSoukenik, M. / Leidert, M. / Sievert, V. / Buessow, K. / Leitner, D. / Labudde, D. / Ball, L.J. / Oschkinat, H.
CitationJournal: FEBS Lett. / Year: 2004
Title: The SEP domain of p47 acts as a reversible competitive inhibitor of cathepsin L
Authors: Soukenik, M. / Diehl, A. / Leidert, M. / Sievert, V. / Buessow, K. / Leitner, D. / Labudde, D. / Ball, L.J. / Lechner, A. / Nagler, D.K. / Oschkinat, H.
History
DepositionMar 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / 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 / _struct_ref_seq_dif.details
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: NSFL1 cofactor p47


Theoretical massNumber of molelcules
Total (without water)11,3681
Polymers11,3681
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NSFL1 cofactor p47 / p47 / p47 protein isoform a / P47 protein / p97 cofactor p47


Mass: 11367.585 Da / Num. of mol.: 1 / Fragment: SEP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNZ2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
2323D 13C-separated NOESY
3433D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM SEP domain U-15N;20mM phosphate buffer NA; 150mM sodium chloride; 90% H2O, 10% D2O90% H2O/10% D2O
21mM SEP domain U-15N,13C;20mM phosphate buffer NA; 150mM sodium chloride; 90% H2O, 10% D2O90% H2O/10% D2O
31mM SEP domain U-15N,13C;20mM phosphate buffer NA; 150mM sodium chloride; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM phosphate buffer NA, 150mM sodium chloride 5.6 ambient 300 K
220mM phosphate buffer NA, 150mM sodium chloride 5.6 ambient 300 K
320mM phosphate buffer NA, 150mM sodium chloride 5.6 ambient 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukerprocessing
PASTE/PAPST1.4Labudde,D., Leitner,D.collection
PLATON2Labudde,D., Leitner,D.data analysis
Sparky3.1data analysis
Aria/CNS1.2Nilges. M.structure solution
Aria/CNS1.2Nilges. M.refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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