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- PDB-9v4e: Crystal Structure of Gallus gallus c-Src Kinase Domain with Point... -

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Basic information

Entry
Database: PDB / ID: 9v4e
TitleCrystal Structure of Gallus gallus c-Src Kinase Domain with Point mutation Y416D and Deletion of Residues N414, T417, and R419 Bound to AMP-PNP
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / tyrosine kinase
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / : / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Degradation of CDH1 / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / : / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / immune system process / 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-cell junction / cell junction / protein tyrosine kinase activity / protein phosphatase binding / cytoskeleton / cell differentiation / cell adhesion / endosome membrane / regulation of cell cycle / mitochondrial inner membrane / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsJain, P. / Clifton, B.E. / Laurino, P.
Funding support Japan, 2items
OrganizationGrant numberCountry
Other private
Japan Society for the Promotion of Science (JSPS)22K15064 Japan
CitationJournal: To Be Published
Title: Crystal Structure of Gallus gallus c-Src Kinase Domain with Point mutation Y416D and Deletion of Residues N414, T417, and R419 Bound to AMP-PNP
Authors: Jain, P. / Clifton, B.E. / Laurino, P.
History
DepositionMay 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7293
Polymers32,1981
Non-polymers5312
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-11 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.457, 62.874, 105.378
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32198.037 Da / Num. of mol.: 1 / Mutation: Y416D/delN414,T417,R419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 5.5
Details: 19% PEG 3350, 5% glycerol, 0.1 M Bis-Tris pH 5.5, and 0.2 M sodium acetate Cryoprotectant: 30% PEG 400, 19% PEG 3350, 5% glycerol, 0.1 M Bis-Tris pH 5.5, and 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→41.46 Å / Num. obs: 27180 / % possible obs: 99.8 % / Redundancy: 8.13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.089 / Net I/σ(I): 19.52
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 8.35 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 4326 / CC1/2: 0.852 / Rrim(I) all: 0.779

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Processing

Software
NameVersionClassification
XDSJun 30, 2024data scaling
XDSJun 30, 2024data reduction
MOLREP11.9.02phasing
REFMAC5.8.0430 (refmacat 0.4.88)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.78→40.416 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.656 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2413 1348 4.96 %
Rwork0.2001 25832 -
all0.202 --
obs-27180 99.776 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.111 Å2
Baniso -1Baniso -2Baniso -3
1-0.159 Å20 Å2-0 Å2
2---0.132 Å2-0 Å2
3----0.027 Å2
Refinement stepCycle: LAST / Resolution: 1.78→40.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 32 94 2051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122007
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161853
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.8392735
X-RAY DIFFRACTIONr_angle_other_deg0.5741.7454274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7495245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.05511
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.02451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59610319
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.5041081
X-RAY DIFFRACTIONr_chiral_restr0.0840.2308
X-RAY DIFFRACTIONr_chiral_restr_other0.0860.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.2240.2421
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21728
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2995
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21030
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.282
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.320.28
X-RAY DIFFRACTIONr_nbd_other0.1880.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.29
X-RAY DIFFRACTIONr_mcbond_it3.233.034989
X-RAY DIFFRACTIONr_mcbond_other3.233.034989
X-RAY DIFFRACTIONr_mcangle_it4.4555.4251228
X-RAY DIFFRACTIONr_mcangle_other4.4545.4241229
X-RAY DIFFRACTIONr_scbond_it3.9973.4341018
X-RAY DIFFRACTIONr_scbond_other3.9973.4341018
X-RAY DIFFRACTIONr_scangle_it5.9376.1981506
X-RAY DIFFRACTIONr_scangle_other5.9356.1971507
X-RAY DIFFRACTIONr_lrange_it7.74931.7482287
X-RAY DIFFRACTIONr_lrange_other7.73831.0472274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.8250.322950.2661865X-RAY DIFFRACTION98.3936
1.825-1.8750.282960.2581836X-RAY DIFFRACTION99.9483
1.875-1.9290.2591060.2321761X-RAY DIFFRACTION99.9465
1.929-1.9880.234910.1971736X-RAY DIFFRACTION99.9453
1.988-2.0530.234920.2041656X-RAY DIFFRACTION100
2.053-2.1250.26960.1891612X-RAY DIFFRACTION100
2.125-2.2050.224820.1851584X-RAY DIFFRACTION99.94
2.205-2.2950.251770.191516X-RAY DIFFRACTION100
2.295-2.3970.219710.1831478X-RAY DIFFRACTION100
2.397-2.5130.185640.1731397X-RAY DIFFRACTION99.9316
2.513-2.6480.216640.1781340X-RAY DIFFRACTION100
2.648-2.8080.213670.1841267X-RAY DIFFRACTION100
2.808-3.0010.25520.2021203X-RAY DIFFRACTION99.9204
3.001-3.240.269550.2041117X-RAY DIFFRACTION99.9147
3.24-3.5470.252480.2091035X-RAY DIFFRACTION99.632
3.547-3.9620.191570.189930X-RAY DIFFRACTION99.8988
3.962-4.5680.229420.172851X-RAY DIFFRACTION99.6652
4.568-5.5770.246380.2714X-RAY DIFFRACTION99.8672
5.577-7.8120.274310.245580X-RAY DIFFRACTION100
7.812-40.4160.319240.263354X-RAY DIFFRACTION99.2126

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