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- PDB-1v38: Solution structure of the Sterile Alpha Motif (SAM) domain of mou... -

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Basic information

Entry
Database: PDB / ID: 1v38
TitleSolution structure of the Sterile Alpha Motif (SAM) domain of mouse SAMSN1
ComponentsSAM-domain protein SAMSN-1
KeywordsSIGNALING PROTEIN / Structural genomics / Hypothetical protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of adaptive immune response / negative regulation of B cell activation / negative regulation of peptidyl-tyrosine phosphorylation / ruffle / phosphotyrosine residue binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SAMSN1, SAM domain / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...SAMSN1, SAM domain / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Src homology 3 domains / DNA polymerase; domain 1 / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SAM domain-containing protein SAMSN-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A. / Kigawa, T. / Koshiba, S. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the Sterile Alpha Motif (SAM) domain of mouse SAMSN1
Authors: Goroncy, A. / Kigawa, T. / Koshiba, S. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S.
History
DepositionOct 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 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: SAM-domain protein SAMSN-1


Theoretical massNumber of molelcules
Total (without water)8,6341
Polymers8,6341
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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein SAM-domain protein SAMSN-1 / SAMSN1 / SAM domain / SH3 domain and nuclear localisation signals protein 1


Mass: 8634.424 Da / Num. of mol.: 1 / Fragment: STERILE ALPHA MOTIF (SAM) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Plasmid: P030120-80 / References: UniProt: P57725

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.19mM SAM domain, 20mM phosphate buffer Na, 100mM NaCl, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERcollection
NMRPipe20020425FRANK DELAGLIOprocessing
NMRView5.0.14BRUCE A. JOHNSONdata analysis
KUJIRA0.811NAOHIRO KOBAYASHIdata analysis
CYANA2.0.15PETER GUENTERTrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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