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- PDB-4f59: Triple mutant Src SH2 domain -

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Basic information

Entry
Database: PDB / ID: 4f59
TitleTriple mutant Src SH2 domain
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / SH2 domain / cell signalling / phosphotyrosine binding
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / 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 integrin activation ...regulation of caveolin-mediated endocytosis / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / 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 integrin activation / BMP receptor binding / negative regulation of focal adhesion assembly / Activated NTRK2 signals through FYN / intestinal epithelial cell development / focal adhesion assembly / Netrin mediated repulsion signals / negative regulation of neutrophil activation / bone resorption / positive regulation of small GTPase mediated signal transduction / connexin binding / Activated NTRK3 signals through PI3K / signal complex assembly / regulation of vascular permeability / Co-stimulation by CD28 / EPH-Ephrin signaling / podosome / positive regulation of lamellipodium morphogenesis / DCC mediated attractive signaling / regulation of bone resorption / Regulation of RUNX1 Expression and Activity / stress fiber assembly / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / leukocyte migration / MET activates PTK2 signaling / Regulation of KIT signaling / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / phospholipase activator activity / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / positive regulation of Rac protein signal transduction / Receptor Mediated Mitophagy / stimulatory C-type lectin receptor signaling pathway / Signaling by EGFR / negative regulation of intrinsic apoptotic signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / regulation of cell-cell adhesion / GRB2:SOS provides linkage to MAPK signaling for Integrins / progesterone receptor signaling pathway / RHOU GTPase cycle / Recycling pathway of L1 / positive regulation of epithelial cell migration / RET signaling / regulation of heart rate by cardiac conduction / FCGR activation / signaling receptor activator activity / negative regulation of anoikis / Long-term potentiation / EPH-ephrin mediated repulsion of cells / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / transforming growth factor beta receptor signaling pathway / GAB1 signalosome / negative regulation of hippo signaling / protein tyrosine kinase activator activity / Nuclear signaling by ERBB4 / T cell costimulation / lactation / osteoclast differentiation / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / Signaling by ERBB2 / Integrin signaling / p38MAPK events / EPHB-mediated forward signaling / positive regulation of TORC1 signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / Downstream signal transduction / FCGR3A-mediated IL10 synthesis / ionotropic glutamate receptor binding / positive regulation of glycolytic process / SH2 domain binding / integrin-mediated signaling pathway / response to interleukin-1 / negative regulation of extrinsic apoptotic signaling pathway / Downregulation of ERBB4 signaling / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / InlA-mediated entry of Listeria monocytogenes into host cells / angiotensin-activated signaling pathway
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 ...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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsKaneko, T. / Huang, H. / Cao, X. / Li, C. / Voss, C. / Sidhu, S.S. / Li, S.S.
CitationJournal: Sci.Signal. / Year: 2012
Title: Superbinder SH2 Domains Act as Antagonists of Cell Signaling.
Authors: Kaneko, T. / Huang, H. / Cao, X. / Li, X. / Li, C. / Voss, C. / Sidhu, S.S. / Li, S.S.
History
DepositionMay 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,6991
Polymers12,6991
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.070, 67.070, 46.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailsbiological unit is the same as asym.

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Components

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


Mass: 12699.316 Da / Num. of mol.: 1 / Fragment: SH2 domain / Mutation: T183V/C188A/K206L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12931
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1 M Tris-HCl, 18% PEG6000, 0.2 M lithium chloride, pH 7.6, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 114 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 26, 2011
RadiationMonochromator: Graded multilayer (osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.706→27.281 Å / Num. all: 13044 / Num. obs: 13044 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.045 / Net I/σ(I): 26.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.795.40.2642.8905416680.26485.9
1.79-1.95.80.1544.71073118530.154100
1.9-2.035.90.0957.11021917460.095100
2.03-2.195.90.06310946316000.063100
2.19-2.460.04813.2897315060.048100
2.4-2.6860.0415814113490.04100
2.68-3.160.03714.9720211920.037100
3.1-3.795.90.04213.2599710100.04299.8
3.79-5.365.50.03915.441317520.03994.2
5.36-27.2815.10.0415.318803680.0480.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å27.28 Å
Translation2 Å27.28 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→27.28 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2692 / WRfactor Rwork: 0.2206 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8318 / SU B: 5.989 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1182 / SU Rfree: 0.1185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 613 4.7 %RANDOM
Rwork0.2045 ---
all0.2064 13019 --
obs0.2064 13019 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.8 Å2 / Biso mean: 34.6901 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.71→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 0 82 949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021884
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9471193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.63722.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35315153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.648158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02671
X-RAY DIFFRACTIONr_mcbond_it0.8871.5534
X-RAY DIFFRACTIONr_mcangle_it1.5112857
X-RAY DIFFRACTIONr_scbond_it2.5423350
X-RAY DIFFRACTIONr_scangle_it4.0084.5336
LS refinement shellResolution: 1.706→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 47 -
Rwork0.385 882 -
all-929 -
obs--96.27 %
Refinement TLS params.Method: refined / Origin x: -8.7844 Å / Origin y: 23.5253 Å / Origin z: -0.0804 Å
111213212223313233
T0.063 Å20.0155 Å20.0121 Å2-0.015 Å2-0.0005 Å2--0.0247 Å2
L4.3213 °2-1.4485 °2-0.0251 °2-3.9521 °20.1409 °2--5.2176 °2
S0.1035 Å °0.1128 Å °0.0478 Å °-0.1507 Å °-0.0601 Å °-0.1067 Å °-0.5143 Å °-0.087 Å °-0.0434 Å °

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