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- PDB-2jyq: NMR structure of the apo v-Src SH2 domain -

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Basic information

Entry
Database: PDB / ID: 2jyq
TitleNMR structure of the apo v-Src SH2 domain
ComponentsTyrosine-protein kinase transforming protein Src
KeywordsTRANSFERASE / PROTEIN / SRC / SH2 / src homology 2 / ATP-binding / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Oncogene / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion ...osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion / phosphorylation / innate immune response / signaling receptor binding / ATP binding
Similarity search - Function
SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily ...SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase transforming protein Src
Similarity search - Component
Biological speciesRous sarcoma virus
MethodSOLUTION NMR / simulated annealing
AuthorsTaylor, J.D. / Ababou, A. / Williams, M.A. / Ladbury, J.E.
CitationJournal: Proteins / Year: 2008
Title: Structure, dynamics, and binding thermodynamics of the v-Src SH2 domain: Implications for drug design
Authors: Taylor, J.D. / Ababou, A. / Fawaz, R.R. / Hobbs, C.J. / Williams, M.A. / Ladbury, J.E.
History
DepositionDec 17, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 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: Tyrosine-protein kinase transforming protein Src


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
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 / 120back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

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Components

#1: Protein Tyrosine-protein kinase transforming protein Src / p60-Src / v-Src / pp60v-src


Mass: 12186.738 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Strain: Schmidt-Ruppin E / Gene: V-SRC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P63185, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1823D HNHA
1923D HNHB
11013D (H)CCH-TOCSY
11123D 1H-15N NOESY
11223D 1H-15N NOESY
11323D 1H-15N TOCSY
11413D 1H-13C NOESY
NMR detailsText: The structure was determined using a combination of NOE and H bonding data

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM [U-100% 13C; U-100% 15N] v-Src SH2 polypeptide, 90% H2O/10% D2O90% H2O/10% D2O
20.5mM [U-100% 15N] v-Src SH2 polypeptide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMv-Src SH2 polypeptide[U-100% 13C; U-100% 15N]1
0.5 mMv-Src SH2 polypeptide[U-100% 15N]2
Sample conditionsIonic strength: 0.05 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityPlusVarianUNITYPLUS5001
Varian UnityPlusVarianUNITYPLUS6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
ANSIGKraulischemical shift assignment
ANSIGKraulispeak picking
ARIA2.2Linge, O'Donoghue, Nilgesautomated noesy assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges, Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Final structures refined in shell of water
NMR constraintsNOE constraints total: 2929 / Hydrogen bond constraints total count: 82
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 120 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.006 Å / Distance rms dev error: 0.001 Å

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