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- PDB-1x69: Solution structures of the SH3 domain of human Src substrate cortactin -

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Basic information

Entry
Database: PDB / ID: 1x69
TitleSolution structures of the SH3 domain of human Src substrate cortactin
Componentscortactin isoform a
KeywordsSIGNALING PROTEIN / SH3 domain / CTTN / Oncogene EMS1 / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


lamellipodium organization / site of polarized growth / mitotic spindle midzone / regulation of mitophagy / profilin binding / positive regulation of smooth muscle contraction / substrate-dependent cell migration, cell extension / focal adhesion assembly / podosome / dendritic spine maintenance ...lamellipodium organization / site of polarized growth / mitotic spindle midzone / regulation of mitophagy / profilin binding / positive regulation of smooth muscle contraction / substrate-dependent cell migration, cell extension / focal adhesion assembly / podosome / dendritic spine maintenance / regulation of axon extension / cortical actin cytoskeleton / cortical cytoskeleton / positive regulation of actin filament polymerization / RHO GTPases activate PAKs / endocytic vesicle / extrinsic apoptotic signaling pathway / clathrin-coated pit / voltage-gated potassium channel complex / ruffle / neuron projection morphogenesis / receptor-mediated endocytosis / cell motility / actin filament / negative regulation of extrinsic apoptotic signaling pathway / intracellular protein transport / actin filament binding / lamellipodium / Clathrin-mediated endocytosis / cell cortex / actin cytoskeleton organization / dendritic spine / cytoskeleton / cadherin binding / intracellular membrane-bounded organelle / focal adhesion / Golgi apparatus / endoplasmic reticulum / signal transduction / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / Variant SH3 domain / SH3 Domains / 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
Src substrate cortactin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structures of the SH3 domain of human Src substrate cortactin
Authors: Sato, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / 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 / _pdbx_nmr_spectrometer.model / _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: cortactin isoform a


Theoretical massNumber of molelcules
Total (without water)8,5971
Polymers8,5971
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein cortactin isoform a / Src substrate cortactin


Mass: 8597.145 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: EMS1 / Plasmid: P040510-08 / References: UniProt: Q14247

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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: 1mM SH3 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 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 / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9295Kobayashi, 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 least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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