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- PDB-8wff: The Crystal Structure of LYN from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wff
TitleThe Crystal Structure of LYN from Biortus.
ComponentsTyrosine-protein kinase Lyn
KeywordsONCOPROTEIN / Transferase Adaptive immunity ATP-binding
Function / homology
Function and homology information


negative regulation of myeloid leukocyte differentiation / C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / response to sterol depletion / regulation of mast cell activation / negative regulation of intracellular signal transduction / positive regulation of oligodendrocyte progenitor proliferation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway ...negative regulation of myeloid leukocyte differentiation / C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / response to sterol depletion / regulation of mast cell activation / negative regulation of intracellular signal transduction / positive regulation of oligodendrocyte progenitor proliferation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / Fc receptor mediated inhibitory signaling pathway / regulation of B cell receptor signaling pathway / negative regulation of toll-like receptor 2 signaling pathway / tolerance induction to self antigen / integrin alpha2-beta1 complex / positive regulation of mast cell proliferation / negative regulation of mast cell proliferation / glycosphingolipid binding / immune response-regulating cell surface receptor signaling pathway / platelet degranulation / positive regulation of amyloid precursor protein catabolic process / regulation of mast cell degranulation / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of immune response / regulation of platelet aggregation / phosphorylation-dependent protein binding / dendritic cell differentiation / regulation of B cell apoptotic process / neuroinflammatory response / phosphatidylinositol 3-kinase activator activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / oligodendrocyte development / Erythropoietin activates Phospholipase C gamma (PLCG) / Platelet Adhesion to exposed collagen / histamine secretion by mast cell / CD22 mediated BCR regulation / regulation of release of sequestered calcium ion into cytosol / response to carbohydrate / gamma-tubulin binding / platelet-derived growth factor receptor binding / Co-stimulation by CD28 / Fc epsilon receptor (FCERI) signaling / EPH-Ephrin signaling / Regulation of KIT signaling / toll-like receptor 4 signaling pathway / postsynaptic specialization, intracellular component / leukocyte migration / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / negative regulation of B cell proliferation / Dectin-2 family / mitochondrial crista / stimulatory C-type lectin receptor signaling pathway / signaling receptor activator activity / Fc-epsilon receptor signaling pathway / regulation of cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / B cell homeostasis / regulation of protein phosphorylation / negative regulation of protein phosphorylation / FCGR activation / growth hormone receptor signaling pathway via JAK-STAT / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of MAP kinase activity / response to amino acid / Role of LAT2/NTAL/LAB on calcium mobilization / response to axon injury / fatty acid transport / hematopoietic progenitor cell differentiation / regulation of ERK1 and ERK2 cascade / Growth hormone receptor signaling / positive regulation of phosphorylation / Signaling by CSF3 (G-CSF) / Erythropoietin activates RAS / GPVI-mediated activation cascade / cellular response to retinoic acid / positive regulation of glial cell proliferation / response to hormone / ephrin receptor binding / T cell costimulation / EPHB-mediated forward signaling / FCERI mediated Ca+2 mobilization / CD209 (DC-SIGN) signaling / regulation of cytokine production / FCGR3A-mediated IL10 synthesis / lipopolysaccharide-mediated signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / cell surface receptor protein tyrosine kinase signaling pathway / erythrocyte differentiation / DNA damage checkpoint signaling / Cell surface interactions at the vascular wall / adherens junction / non-membrane spanning protein tyrosine kinase activity
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / 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
Similarity search - Domain/homology
CITRATE ANION / Tyrosine-protein kinase Lyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Lu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of LYN from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Lu, Y.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 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 Lyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5634
Polymers7,3031
Non-polymers2603
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area4130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.730, 45.730, 56.686
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tyrosine-protein kinase Lyn


Mass: 7303.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYN / Production host: Escherichia coli (E. coli) / References: UniProt: P07948
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Citric acid pH3.5, 3.0M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.3→39.603 Å / Num. obs: 16562 / % possible obs: 99.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.2
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.293 / Num. unique obs: 790

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.603 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.162 / SU B: 1.615 / SU ML: 0.031 / Average fsc free: 0.9548 / Average fsc work: 0.9654 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1822 806 4.876 %
Rwork0.1552 15723 -
all0.157 --
obs-16529 99.668 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.955 Å2
Baniso -1Baniso -2Baniso -3
1--0.446 Å2-0.223 Å2-0 Å2
2---0.446 Å20 Å2
3---1.447 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms506 0 15 79 600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013544
X-RAY DIFFRACTIONr_bond_other_d0.0020.017519
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.637737
X-RAY DIFFRACTIONr_angle_other_deg1.4211.5941212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.909566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5926.08723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09815101
X-RAY DIFFRACTIONr_chiral_restr0.090.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02107
X-RAY DIFFRACTIONr_nbd_refined0.1810.2104
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.2426
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2253
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2243
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.243
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.27
X-RAY DIFFRACTIONr_nbd_other0.2250.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.212
X-RAY DIFFRACTIONr_mcbond_it1.6061.148255
X-RAY DIFFRACTIONr_mcbond_other1.5721.141254
X-RAY DIFFRACTIONr_mcangle_it2.3491.726318
X-RAY DIFFRACTIONr_mcangle_other2.371.732319
X-RAY DIFFRACTIONr_scbond_it2.0741.553289
X-RAY DIFFRACTIONr_scbond_other2.0611.554288
X-RAY DIFFRACTIONr_scangle_it2.5242.202417
X-RAY DIFFRACTIONr_scangle_other2.5212.208418
X-RAY DIFFRACTIONr_lrange_it4.41916.61621
X-RAY DIFFRACTIONr_lrange_other3.7615.942610
X-RAY DIFFRACTIONr_rigid_bond_restr2.74531063
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
1.3-1.3340.335500.22911300.23311990.9520.95998.41530.213
1.334-1.370.201530.18511440.18612050.9570.94899.33610.172
1.37-1.410.206700.15810860.1611570.9310.94699.91360.144
1.41-1.4530.203520.14210810.14511330.9330.961000.13
1.453-1.5010.179410.11910300.12110710.9580.9721000.111
1.501-1.5530.175560.11510060.11910620.9630.9721000.11
1.553-1.6120.181390.1159720.11710110.9440.9781000.114
1.612-1.6780.145540.1139380.1159920.9660.9791000.113
1.678-1.7520.195360.1299120.1319480.9640.9731000.133
1.752-1.8370.184400.1348560.1368960.9470.9731000.142
1.837-1.9370.129500.1338000.1328500.9770.9781000.144
1.937-2.0540.171310.1427820.1438130.9640.9721000.162
2.054-2.1950.168350.1447310.1457660.9710.9691000.164
2.195-2.370.19490.1486530.1517020.9610.9671000.175
2.37-2.5960.183430.1566150.1586580.9520.9591000.187
2.596-2.9010.234260.1765770.1786030.9230.9551000.215
2.901-3.3460.186280.1744920.1755200.9610.9581000.215
3.346-4.0910.149300.1624130.1614440.9710.96699.77480.202
4.091-5.7550.174160.1843300.1833550.9750.9797.46480.243
5.755-39.6030.34570.2741740.2771980.9230.93891.41410.308

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