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- PDB-2dl0: Solution structure of the SAM-domain of the SAM and SH3 domain co... -

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Basic information

Entry
Database: PDB / ID: 2dl0
TitleSolution structure of the SAM-domain of the SAM and SH3 domain containing protein 1
ComponentsSAM and SH3 domain-containing protein 1
KeywordsSIGNALING PROTEIN / CELL-FREE PROTEIN SYNTHESIS / PROTEIN REGULATION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of protein K63-linked ubiquitination / regulation of protein autoubiquitination / regulation of epithelial cell migration / positive regulation of lipopolysaccharide-mediated signaling pathway / mitogen-activated protein kinase kinase kinase binding / positive regulation of p38MAPK cascade / G-protein alpha-subunit binding / positive regulation of JUN kinase activity / positive regulation of endothelial cell migration / positive regulation of non-canonical NF-kappaB signal transduction ...regulation of protein K63-linked ubiquitination / regulation of protein autoubiquitination / regulation of epithelial cell migration / positive regulation of lipopolysaccharide-mediated signaling pathway / mitogen-activated protein kinase kinase kinase binding / positive regulation of p38MAPK cascade / G-protein alpha-subunit binding / positive regulation of JUN kinase activity / positive regulation of endothelial cell migration / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / positive regulation of angiogenesis / molecular adaptor activity / protein kinase binding / protein-containing complex / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
SAM and SH3 domain-containing protein 1, SH3 domain / SASH1, SAM domain repeat 1 / SASH1, SAM domain repeat 2 / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. ...SAM and SH3 domain-containing protein 1, SH3 domain / SASH1, SAM domain repeat 1 / SASH1, SAM domain repeat 2 / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / 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 and SH3 domain-containing protein 1 / Uncharacterized protein DKFZp686I1750
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SAM-domain of the SAM and SH3 domain containing protein 1
Authors: Goroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 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 and SH3 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)9,8831
Polymers9,8831
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)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein SAM and SH3 domain-containing protein 1 / Proline-glutamate repeat-containing protein


Mass: 9883.243 Da / Num. of mol.: 1 / Fragment: sam domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: SASH1 / Plasmid: P050719-14 / Production host: Cell free synthesis / References: UniProt: O94885, UniProt: Q7Z3N8*PLUS

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.18mM SAM DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02 % NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: AMBIENT / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.32P.GUNTERT ET AL.refinement
CYANA2.0.32P.GUNTERT ET AL.structure solution
TopSpin1.3BRUKERcollection
NMRPipe20060324aFRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.899aNAOHIRO KOBAYASHIdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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