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- PDB-2nwm: Solution structure of the first SH3 domain of human Vinexin and i... -

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Basic information

Entry
Database: PDB / ID: 2nwm
TitleSolution structure of the first SH3 domain of human Vinexin and its interaction with the peptides from Vinculin
ComponentsVinexin
KeywordsCELL ADHESION / Vinexin SH3 domain
Function / homology
Function and homology information


positive regulation of cytoskeleton organization / cell-substrate junction / vinculin binding / cell-substrate adhesion / Smooth Muscle Contraction / positive regulation of stress fiber assembly / structural constituent of cytoskeleton / MAPK cascade / cytoskeleton / positive regulation of MAPK cascade ...positive regulation of cytoskeleton organization / cell-substrate junction / vinculin binding / cell-substrate adhesion / Smooth Muscle Contraction / positive regulation of stress fiber assembly / structural constituent of cytoskeleton / MAPK cascade / cytoskeleton / positive regulation of MAPK cascade / cell adhesion / focal adhesion / negative regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
Similarity search - Function
Vinexin, SH3 domain 3 / Vinexin, SH3 domain 2 / Vinexin, SH3 domain 1 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / : / Variant SH3 domain / SH3 Domains ...Vinexin, SH3 domain 3 / Vinexin, SH3 domain 2 / Vinexin, SH3 domain 1 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / : / Variant SH3 domain / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsZhang, J. / Yao, B. / Wu, J. / Shi, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Solution structure of the first SH3 domain of human vinexin and its interaction with vinculin peptides
Authors: Zhang, J. / Li, X. / Yao, B. / Shen, W. / Sun, H. / Xu, C. / Wu, J. / Shi, Y.
History
DepositionNov 15, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: Vinexin


Theoretical massNumber of molelcules
Total (without water)7,6891
Polymers7,6891
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Vinexin / Sorbin and SH3 domain-containing protein 3 / SH3-containing adapter molecule 1 / SCAM-1


Mass: 7688.761 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Vinexin / Plasmid: PET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60504

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-1.2mM 15N, 13C-labeled human Vinexin SH3 domain; 50mM phosphate buffer(pH 6.2); 50mM NaCl; 1mM DTT; 1mM EDTA; 90% H2O, 10% D2O90% H2O/10% D2O
21-1.2mM 15N, 13C-labeled human Vinexin SH3 domain; 50mM phosphate buffer(pH 6.2); 50mM NaCl; 1mM DTT; 1mM EDTA; 99.96% D2O99.96% D2O
Sample conditionspH: 6.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglio, F.processing
Sparky3Goddard, T.D., Kneller, D.G.data analysis
CNS1.1structure solution
MOLMOL2K.2Koradidata analysis
CNS1.1refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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