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- PDB-2dl3: Solution structure of the first SH3 domain of human sorbin and Sh... -

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Basic information

Entry
Database: PDB / ID: 2dl3
TitleSolution structure of the first SH3 domain of human sorbin and Sh3 domain-containing protein 1
ComponentsSorbin and SH3 domain-containing protein 1
KeywordsCELL ADHESION / SIGNALING PROTEIN / SH3 domain / Sorbin and SH3 domain-containing protein 1 / Ponsin / c-Cbl-associated protein / CAP / SH3 domain protein 5 / SH3P12 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cell-substrate junction / zonula adherens / flotillin complex / focal adhesion assembly / cell-substrate adhesion / stress fiber assembly / positive regulation of glycogen biosynthetic process / Smooth Muscle Contraction / positive regulation of lipid biosynthetic process / positive regulation of insulin receptor signaling pathway ...cell-substrate junction / zonula adherens / flotillin complex / focal adhesion assembly / cell-substrate adhesion / stress fiber assembly / positive regulation of glycogen biosynthetic process / Smooth Muscle Contraction / positive regulation of lipid biosynthetic process / positive regulation of insulin receptor signaling pathway / stress fiber / cytoskeletal protein binding / cell-matrix adhesion / positive regulation of glucose import / positive regulation of protein localization to plasma membrane / adherens junction / insulin receptor binding / nuclear matrix / cellular response to insulin stimulus / signaling receptor complex adaptor activity / insulin receptor signaling pathway / actin binding / membrane raft / focal adhesion / centrosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Variant SH3 domain / Variant SH3 domain / SH3 Domains ...c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Variant SH3 domain / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Sorbin and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.R. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the first SH3 domain of human sorbin and Sh3 domain-containing protein 1
Authors: Qin, X.R. / Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 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: Sorbin and SH3 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)7,5941
Polymers7,5941
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Sorbin and SH3 domain-containing protein 1 / Ponsin / c-Cbl-associated protein / CAP / SH3 domain protein 5 / SH3P12


Mass: 7594.495 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: SORBS1, KIAA1296, SH3D5 / Plasmid: P050613-04 / Production host: Cell free synthesis / References: UniProt: Q9BX66

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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
NMR detailsText: spectrometer_id 1 for 3D_15N_separated_NOESY; spectrometer_id 2 for 3D_13C_separated_NOESY

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Sample preparation

DetailsContents: 1.00mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 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: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9296Kobayashi,N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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