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- PDB-8xn8: The Crystal Structure of SRC from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xn8
TitleThe Crystal Structure of SRC from Biortus.
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsSIGNALING PROTEIN / Kinase / Transferase / Cell adhesion / ATP-binding
Function / homology
Function and homology information


Activated NTRK3 signals through PI3K / Regulation of gap junction activity / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / Nuclear signaling by ERBB4 / Signaling by EGFR / positive regulation of male germ cell proliferation / DCC mediated attractive signaling / dendritic filopodium / Ephrin signaling ...Activated NTRK3 signals through PI3K / Regulation of gap junction activity / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / Nuclear signaling by ERBB4 / Signaling by EGFR / positive regulation of male germ cell proliferation / DCC mediated attractive signaling / dendritic filopodium / Ephrin signaling / VEGFR2 mediated cell proliferation / PECAM1 interactions / MET activates PTK2 signaling / Signaling by ERBB2 / Regulation of KIT signaling / GAB1 signalosome / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Co-stimulation by CD28 / mitochondrion-derived vesicle / Downstream signal transduction / EPH-ephrin mediated repulsion of cells / primary ovarian follicle growth / neuron to neuron synapse / Signaling by SCF-KIT / Downregulation of ERBB4 signaling / FCGR activation / Spry regulation of FGF signaling / RAF activation / Thrombin signalling through proteinase activated receptors (PARs) / EPHB-mediated forward signaling / positive regulation of protein transport / Regulation of RUNX3 expression and activity / regulation of caveolin-mediated endocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / MAP2K and MAPK activation / Cyclin D associated events in G1 / positive regulation of ovarian follicle development / Extra-nuclear estrogen signaling / regulation of cell projection assembly / PIP3 activates AKT signaling / Recycling pathway of L1 / Degradation of CDH1 / regulation of epithelial cell migration / negative regulation of telomere maintenance / CLEC7A (Dectin-1) signaling / RHO GTPases Activate Formins / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of glucose metabolic process / positive regulation of protein processing / toll-like receptor 3 signaling pathway / transcytosis / RET signaling / ADP signalling through P2Y purinoceptor 1 / BMP receptor binding / negative regulation of focal adhesion assembly / G alpha (i) signalling events / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / focal adhesion assembly / positive regulation of small GTPase mediated signal transduction / connexin binding / VEGFA-VEGFR2 Pathway / osteoclast development / cellular response to fluid shear stress / positive regulation of bone resorption / branching involved in mammary gland duct morphogenesis / podosome / positive regulation of neural precursor cell proliferation / positive regulation of podosome assembly / positive regulation of lamellipodium morphogenesis / positive regulation of Ras protein signal transduction / postsynaptic specialization, intracellular component / negative regulation of mitochondrial depolarization / odontogenesis / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / positive regulation of smooth muscle cell migration / phospholipase activator activity / interleukin-6-mediated signaling pathway / DNA biosynthetic process / positive regulation of wound healing / stress fiber assembly / positive regulation of Notch signaling pathway / oogenesis / neurotrophin TRK receptor signaling pathway / dendritic growth cone / forebrain development / uterus development / negative regulation of intrinsic apoptotic signaling pathway / regulation of cell-cell adhesion / progesterone receptor signaling pathway / TORC1 signaling
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
ADENOSINE-5'-DIPHOSPHATE / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of SRC from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
History
DepositionDec 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary
Category: pdbx_contact_author / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_contact_author.email / _pdbx_entry_details.has_protein_modification

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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)52,2275
Polymers51,6211
Non-polymers6064
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-16 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.204, 87.468, 105.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 51621.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Src / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P05480, non-specific protein-tyrosine kinase

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Non-polymers , 5 types, 418 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M KNO3 HCl pH6.9, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953702 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953702 Å / Relative weight: 1
ReflectionResolution: 1.95→46.133 Å / Num. obs: 35414 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.3
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.986 / Num. unique obs: 2453

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.133 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.176 / SU B: 4.127 / SU ML: 0.115 / Average fsc free: 0.9207 / Average fsc work: 0.9332 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2242 1682 4.75 %
Rwork0.1847 33732 -
all0.187 --
obs-35414 99.977 %
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: 28.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å2-0 Å2
2---0.153 Å20 Å2
3---0.432 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 38 414 4072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133781
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173513
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.6565129
X-RAY DIFFRACTIONr_angle_other_deg1.2541.5778108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27821.854205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47615648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2161528
X-RAY DIFFRACTIONr_chiral_restr0.0560.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02894
X-RAY DIFFRACTIONr_nbd_refined0.1920.2749
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.23396
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21819
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21772
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2365
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1930.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.217
X-RAY DIFFRACTIONr_nbd_other0.2070.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.225
X-RAY DIFFRACTIONr_mcbond_it1.8052.7811811
X-RAY DIFFRACTIONr_mcbond_other1.8042.7791810
X-RAY DIFFRACTIONr_mcangle_it2.9384.1622265
X-RAY DIFFRACTIONr_mcangle_other2.9374.1652266
X-RAY DIFFRACTIONr_scbond_it2.1613.0661970
X-RAY DIFFRACTIONr_scbond_other2.163.0661971
X-RAY DIFFRACTIONr_scangle_it3.5614.4852858
X-RAY DIFFRACTIONr_scangle_other3.564.4852859
X-RAY DIFFRACTIONr_lrange_it5.68433.2474457
X-RAY DIFFRACTIONr_lrange_other5.56232.7684355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3111140.2592453X-RAY DIFFRACTION100
2.001-2.0550.2541190.2342414X-RAY DIFFRACTION100
2.055-2.1150.2361030.2152339X-RAY DIFFRACTION100
2.115-2.180.241220.2062255X-RAY DIFFRACTION99.9159
2.18-2.2510.2611170.2082194X-RAY DIFFRACTION100
2.251-2.330.2531160.1972120X-RAY DIFFRACTION100
2.33-2.4180.2391070.1892046X-RAY DIFFRACTION100
2.418-2.5170.252810.1831992X-RAY DIFFRACTION100
2.517-2.6280.24850.1781911X-RAY DIFFRACTION100
2.628-2.7570.2561040.1951816X-RAY DIFFRACTION100
2.757-2.9050.277890.1921736X-RAY DIFFRACTION99.9452
2.905-3.0810.211900.1821634X-RAY DIFFRACTION100
3.081-3.2940.239860.1791552X-RAY DIFFRACTION100
3.294-3.5570.221680.1761454X-RAY DIFFRACTION100
3.557-3.8950.191510.1611374X-RAY DIFFRACTION100
3.895-4.3530.185660.1541223X-RAY DIFFRACTION99.9225
4.353-5.0230.182550.1581091X-RAY DIFFRACTION100
5.023-6.1430.179480.183932X-RAY DIFFRACTION100
6.143-8.6520.206450.175744X-RAY DIFFRACTION100
8.652-46.1330.158160.193453X-RAY DIFFRACTION99.1543

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