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- PDB-4f5b: Triple mutant Src SH2 domain bound to phosphotyrosine -

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Basic information

Entry
Database: PDB / ID: 4f5b
TitleTriple mutant Src SH2 domain bound to phosphotyrosine
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / SH2 domain / Cell signalling / phosphotyrosine
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of dephosphorylation / regulation of epithelial cell migration / ERBB2 signaling pathway / positive regulation of protein transport / Regulation of gap junction activity / cellular response to progesterone stimulus / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / positive regulation of integrin activation / Activated NTRK2 signals through FYN / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / regulation of vascular permeability / negative regulation of neutrophil activation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / connexin binding / focal adhesion assembly / cellular response to fluid shear stress / adherens junction organization / signal complex assembly / positive regulation of small GTPase mediated signal transduction / Co-stimulation by CD28 / branching involved in mammary gland duct morphogenesis / response to acidic pH / positive regulation of Ras protein signal transduction / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / positive regulation of podosome assembly / EPH-Ephrin signaling / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / myoblast proliferation / Signal regulatory protein family interactions / cellular response to peptide hormone stimulus / negative regulation of mitochondrial depolarization / podosome / odontogenesis / MET activates PTK2 signaling / cellular response to fatty acid / Regulation of KIT signaling / postsynaptic specialization, intracellular component / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / oogenesis / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / EPHA-mediated growth cone collapse / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / DNA biosynthetic process / positive regulation of Notch signaling pathway / Signaling by EGFR / stress fiber assembly / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / uterus development / regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / PECAM1 interactions / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / dendritic growth cone / protein tyrosine kinase activator activity / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of anoikis / RET signaling / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / GAB1 signalosome / positive regulation of protein serine/threonine kinase activity / negative regulation of hippo signaling
Similarity search - Function
SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains ...SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
O-PHOSPHOTYROSINE / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9602
Polymers12,6991
Non-polymers2611
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.600, 67.600, 46.800
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: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO6P / Details: phosphorylated tyrosine
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
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: Oct 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: 1.57→19.514 Å / Num. all: 15470 / Num. obs: 15470 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rsym value: 0.045 / Net I/σ(I): 30.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.57-1.6580.2662.91993224980.266100
1.65-1.768.10.1714.41724621250.17190.4
1.76-1.888.20.1086.81836022370.108100
1.88-2.0380.0867.11142414290.08670.3
2.03-2.228.40.05131436517070.0589.3
2.22-2.488.30.04413.81243314900.04486.5
2.48-2.878.60.03517.51181013720.03590
2.87-3.518.70.035151061712270.03595
3.51-4.968.20.0414.970248540.0484.3
4.96-20.0047.60.04513.140505310.04592.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.87 Å22.09 Å
Translation1.87 Å22.09 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: 1.57→19.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2377 / WRfactor Rwork: 0.2035 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8507 / SU B: 3.504 / SU ML: 0.057 / SU R Cruickshank DPI: 0.1005 / SU Rfree: 0.0995 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 724 4.7 %RANDOM
Rwork0.1981 ---
all0.1996 15437 --
obs0.1996 15437 90.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.56 Å2 / Biso mean: 24.6385 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.57→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 17 123 1007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021901
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9581217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.28922.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89815154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.776158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02683
X-RAY DIFFRACTIONr_mcbond_it0.8331.5539
X-RAY DIFFRACTIONr_mcangle_it1.5012864
X-RAY DIFFRACTIONr_scbond_it2.43362
X-RAY DIFFRACTIONr_scangle_it3.8324.5353
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 59 -
Rwork0.298 1219 -
all-1278 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.946 Å / Origin y: 23.559 Å / Origin z: -0.158 Å
111213212223313233
T0.096 Å20.0059 Å20.0117 Å2-0.1006 Å20.0086 Å2--0.1439 Å2
L2.0918 °2-1.2259 °20.0742 °2-1.428 °20.2568 °2--1.3051 °2
S0.0347 Å °0.0102 Å °-0.0437 Å °-0.0841 Å °-0.023 Å °0.003 Å °-0.1222 Å °-0.0054 Å °-0.0117 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1000
2X-RAY DIFFRACTION1A1 - 1000

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