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- PDB-9ns1: Intermediate state of Src kinase domain -

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Basic information

Entry
Database: PDB / ID: 9ns1
TitleIntermediate state of Src kinase domain
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsSIGNALING PROTEIN / Intermediate state / kinase src
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity ...regulation of caveolin-mediated endocytosis / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of protein processing / positive regulation of integrin activation / BMP receptor binding / negative regulation of focal adhesion assembly / Activated NTRK2 signals through FYN / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / Netrin mediated repulsion signals / negative regulation of neutrophil activation / focal adhesion assembly / positive regulation of small GTPase mediated signal transduction / connexin binding / osteoclast development / cellular response to fluid shear stress / Activated NTRK3 signals through PI3K / signal complex assembly / regulation of vascular permeability / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / EPH-Ephrin signaling / podosome / DCC mediated attractive signaling / positive regulation of podosome assembly / positive regulation of lamellipodium morphogenesis / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / odontogenesis / MET activates PTK2 signaling / Regulation of KIT signaling / leukocyte migration / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / canonical glycolysis / phospholipase activator activity / EPHA-mediated growth cone collapse / Co-inhibition by CTLA4 / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / Receptor Mediated Mitophagy / stress fiber assembly / oogenesis / positive regulation of Notch signaling pathway / Signaling by EGFR / stimulatory C-type lectin receptor signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / uterus development / forebrain development / PECAM1 interactions / negative regulation of intrinsic apoptotic signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of cell-cell adhesion / RHOU GTPase cycle / progesterone receptor signaling pathway / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / FCGR activation / signaling receptor activator activity / protein tyrosine kinase activator activity / RET signaling / negative regulation of anoikis / positive regulation of epithelial cell migration / Long-term potentiation / EPH-ephrin mediated repulsion of cells / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / bone resorption / GAB1 signalosome / negative regulation of hippo signaling / Nuclear signaling by ERBB4 / positive regulation of Rac protein signal transduction / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / Integrin signaling / p38MAPK events / peptidyl-tyrosine phosphorylation / EPHB-mediated forward signaling / substrate adhesion-dependent cell spreading / positive regulation of TORC1 signaling / transforming growth factor beta receptor signaling pathway
Similarity search - Function
: / 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 / 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
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsCui, Y. / Ali, R. / Clay, M. / Rossi, P. / Liu, A. / Yang, D. / Gough, N. / Geiger, T. / Kalodimos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122462 United States
CitationJournal: Science / Year: 2025
Title: Conformational landscape adaptations enable processive phosphorylation by Src family kinases.
Authors: Cui, Y. / Ali, R. / Clay, M. / Rossi, P. / Liu, A. / Yang, D. / Gough, N.R. / Geiger, T. / Kalodimos, C.G.
History
DepositionMar 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)32,7401
Polymers32,7401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 32739.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Escherichia coli (E. coli)
References: UniProt: P12931, non-specific protein-tyrosine kinase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
116isotropic12D 1H-13C HSQC
126isotropic12D 1H-13C HSQC aromatic
136isotropic12D 1H-15N HSQC
146isotropic13D 1H-15N NOESY
156isotropic13D 1H-13C NOESY
166isotropic13D 1H-13C NOESY aromatic
176isotropic13D CCH NOESY
185isotropic23D HNCA
195isotropic23D HN(CA)CB
1105isotropic23D HNCO
1115isotropic22D 1H-15N HSQC
1125isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetails (eV)LabelSolvent system
solution5250 uM [U-13C; U-15N; U-2H] SrcA311I kinase, 25 mM potassium chloride, 500 mM sodium chloride, 3 mM BME, 1 mM EDTA, 90% H2O/10% D2O15N- 13C- 2Htriple90% H2O/10% D2O
solution6250 uM [U-15N; U-2H] ILVMAT CH3 FY CEHE SrcA311I kinase, 25 mM potassium chloride, 500 mM sodium chloride, 3 mM BME, 1 mM EDTA, 90% H2O/10% D2O15N- ILVMAT 13CH3 FY CE12HE1215N_methyl_FY90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMSrcA311I kinase[U-13C; U-15N; U-2H]5
25 mMpotassium chloridenatural abundance5
500 mMsodium chloridenatural abundance5
3 mMBMEnatural abundance5
1 mMEDTAnatural abundance5
250 uMSrcA311I kinase[U-15N; U-2H] ILVMAT CH3 FY CEHE6
25 mMpotassium chloridenatural abundance6
500 mMsodium chloridenatural abundance6
3 mMBMEnatural abundance6
1 mMEDTAnatural abundance6
Sample conditionsIonic strength: 500 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Bruker AVANCE NEOBrukerAVANCE NEO7002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
PSVSBhattacharya and Montelionegeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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