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- PDB-8x5k: The Crystal Structure of SYK from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x5k
TitleThe Crystal Structure of SYK from Biortus.
ComponentsTyrosine-protein kinase SYK
KeywordsTRANSFERASE / Kinase Adaptive immunity
Function / homology
Function and homology information


interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / cellular response to lectin / B cell receptor complex / regulation of platelet aggregation ...interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / cellular response to lectin / B cell receptor complex / regulation of platelet aggregation / Toll-like receptor binding / serotonin secretion by platelet / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / positive regulation of mast cell cytokine production / neutrophil activation involved in immune response / cell surface pattern recognition receptor signaling pathway / positive regulation of mast cell degranulation / lymph vessel development / collagen-activated tyrosine kinase receptor signaling pathway / regulation of platelet activation / cell activation / beta selection / cellular response to molecule of fungal origin / FLT3 signaling through SRC family kinases / early phagosome / leukotriene biosynthetic process / regulation of phagocytosis / macrophage activation involved in immune response / regulation of tumor necrosis factor-mediated signaling pathway / interleukin-3-mediated signaling pathway / positive regulation of monocyte chemotactic protein-1 production / cellular response to lipid / regulation of DNA-binding transcription factor activity / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of cell adhesion mediated by integrin / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / T cell receptor complex / mast cell degranulation / Dectin-2 family / positive regulation of interleukin-4 production / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / amyloid-beta clearance / positive regulation of interleukin-10 production / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of type I interferon production / Role of phospholipids in phagocytosis / positive regulation of bone resorption / phosphatase binding / regulation of ERK1 and ERK2 cascade / Signaling by CSF3 (G-CSF) / GPVI-mediated activation cascade / neutrophil chemotaxis / phosphotyrosine residue binding / positive regulation of interleukin-12 production / positive regulation of TORC1 signaling / Integrin signaling / FCERI mediated Ca+2 mobilization / B cell differentiation / SH2 domain binding / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of superoxide anion generation / animal organ morphogenesis / integrin-mediated signaling pathway / positive regulation of interleukin-8 production / non-membrane spanning protein tyrosine kinase activity / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / negative regulation of inflammatory response to antigenic stimulus / calcium-mediated signaling / Inactivation of CSF3 (G-CSF) signaling / peptidyl-tyrosine phosphorylation / receptor internalization / Regulation of actin dynamics for phagocytic cup formation / platelet activation / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / cellular response to amyloid-beta / protein import into nucleus / positive regulation of tumor necrosis factor production / kinase activity / integrin binding
Similarity search - Function
Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain ...Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 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
Similarity search - Domain/homology
Chem-3YT / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of SYK from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
History
DepositionNov 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase SYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0093
Polymers32,5541
Non-polymers4562
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.095, 83.903, 39.962
Angle α, β, γ (deg.)90.000, 101.519, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase SYK


Mass: 32553.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43405
#2: Chemical ChemComp-3YT / 2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide


Mass: 393.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N9O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 36.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1M Bis-Tris pH6.5, 25% 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: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.8→41.951 Å / Num. obs: 22844 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.763 / Num. unique obs: 1374

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.951 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.947 / SU ML: 0.119 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.244 1118 4.899 %
Rwork0.1894 21702 -
all0.192 --
obs-22820 99.886 %
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: 32.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.903 Å2-0 Å2-1.396 Å2
2---1.725 Å2-0 Å2
3----0.562 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 33 127 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132238
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162124
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.6453015
X-RAY DIFFRACTIONr_angle_other_deg1.2171.5844896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74922.966118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2091512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_nbd_refined0.1890.2449
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.22046
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21091
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.223
X-RAY DIFFRACTIONr_nbd_other0.1630.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.214
X-RAY DIFFRACTIONr_mcbond_it1.8893.2341057
X-RAY DIFFRACTIONr_mcbond_other1.8893.2311056
X-RAY DIFFRACTIONr_mcangle_it2.9014.8311317
X-RAY DIFFRACTIONr_mcangle_other2.94.8351318
X-RAY DIFFRACTIONr_scbond_it2.2133.5511181
X-RAY DIFFRACTIONr_scbond_other2.2123.5521182
X-RAY DIFFRACTIONr_scangle_it3.5585.2121696
X-RAY DIFFRACTIONr_scangle_other3.5575.2131697
X-RAY DIFFRACTIONr_lrange_it5.22237.542605
X-RAY DIFFRACTIONr_lrange_other5.19737.3742584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.283850.27615920.27616780.8290.83199.94040.276
1.847-1.8970.286670.25515990.25716660.8290.8461000.255
1.897-1.9520.293770.23114980.23415760.8340.86999.93660.231
1.952-2.0120.264840.23514590.23615450.8590.88199.87060.235
2.012-2.0780.297580.22814370.23114960.8660.88199.93320.228
2.078-2.1510.285680.22313940.22514620.8720.8971000.223
2.151-2.2320.262740.21613250.21914020.8940.90999.7860.216
2.232-2.3220.26630.20412790.20713430.9030.91499.92550.204
2.322-2.4250.263670.20112090.20412760.90.9111000.201
2.425-2.5430.318620.19912050.20512670.8760.9211000.199
2.543-2.680.219440.19411170.19511610.920.9291000.194
2.68-2.8420.297570.18410540.18911120.8890.93799.91010.184
2.842-3.0370.214520.19510000.19610520.9240.9311000.195
3.037-3.2790.261650.1959140.29800.9140.93699.8980.195
3.279-3.590.223730.188340.1839090.9380.94899.780.18
3.59-4.010.203320.1617770.1638170.9490.95999.02080.161
4.01-4.6240.218290.1516900.1547230.9450.96599.44670.151
4.624-5.6460.172210.1615990.1616200.9490.9651000.161
5.646-7.9130.342280.1794500.1864780.9410.9631000.179
7.913-41.9510.115120.1722700.1692820.980.9641000.172

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