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- PDB-2mox: solution structure of tandem SH3 domain of Sorbin and SH3 domain-... -

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Basic information

Entry
Database: PDB / ID: 2mox
Titlesolution structure of tandem SH3 domain of Sorbin and SH3 domain-containing protein 1
ComponentsSorbin and SH3 domain-containing protein 1
KeywordsSIGNALING PROTEIN / focal adhesion
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 / na
Model detailslowest energy, model1
AuthorsZhao, D. / Wang, C. / Zhang, J. / Wu, J. / Shi, Y. / Zhang, Z. / Gong, Q.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Structural investigation of the interaction between the tandem SH3 domains of c-Cbl-associated protein and vinculin
Authors: Zhao, D. / Wang, X. / Peng, J. / Wang, C. / Li, F. / Sun, Q. / Zhang, Y. / Zhang, J. / Cai, G. / Zuo, X. / Wu, J. / Shi, Y. / Zhang, Z. / Gong, Q.
History
DepositionMay 7, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)16,6631
Polymers16,6631
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 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 16663.074 Da / Num. of mol.: 1 / Fragment: UNP residues 791-930
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORBS1, KIAA0894, KIAA1296, SH3D5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BX66

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HNCO
1423D CBCA(CO)NH
1523D HBHA(CO)NH
1623D HN(CO)CA
1723D H(CCO)NH
1833D 1H-15N NOESY
1933D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate-1, 0.5 mM [U-100% 15N] protein-2, 1 mM EDTA-3, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium phosphate-4, 1 mM EDTA-5, 0.5 mM [U-100% 13C; U-100% 15N] protein-6, 90% H2O/10% D2O90% H2O/10% D2O
350 mM sodium phosphate-7, 1 mM EDTA-8, 0.5 mM [U-100% 13C; U-100% 15N] protein-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
0.5 mMprotein-2[U-100% 15N]1
1 mMEDTA-31
50 mMsodium phosphate-42
1 mMEDTA-52
0.5 mMprotein-6[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate-73
1 mMEDTA-83
0.5 mMprotein-9[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddarddata analysis
CNSrefinement
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20 / Representative conformer: 1

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