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- PDB-7sa7: Crystal structure of the apo SH2 domains of Syk -

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Basic information

Entry
Database: PDB / ID: 7sa7
TitleCrystal structure of the apo SH2 domains of Syk
ComponentsTyrosine-protein kinase SYK
KeywordsTRANSFERASE / kinase / SH2 domain
Function / homology
Function and homology information


serotonin secretion by platelet / interleukin-15 receptor binding / positive regulation of interleukin-3 production / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / B cell receptor complex ...serotonin secretion by platelet / interleukin-15 receptor binding / positive regulation of interleukin-3 production / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / neutrophil activation involved in immune response / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / positive regulation of mast cell cytokine production / regulation of platelet activation / lymph vessel development / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of mast cell degranulation / macrophage activation involved in immune response / beta selection / regulation of phagocytosis / positive regulation of killing of cells of another organism / leukotriene biosynthetic process / cellular response to molecule of fungal origin / regulation of tumor necrosis factor-mediated signaling pathway / FLT3 signaling through SRC family kinases / early phagosome / interleukin-3-mediated signaling pathway / cellular response to lipid / positive regulation of monocyte chemotactic protein-1 production / regulation of DNA-binding transcription factor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of granulocyte macrophage colony-stimulating factor production / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / T cell receptor complex / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / mast cell degranulation / Fc-gamma receptor signaling pathway involved in phagocytosis / Dectin-2 family / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / phospholipase binding / positive regulation of interleukin-10 production / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / FCGR activation / positive regulation of type I interferon production / positive regulation of interleukin-4 production / positive regulation of bone resorption / phosphatase binding / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of calcium-mediated signaling / Signaling by CSF3 (G-CSF) / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / positive regulation of TORC1 signaling / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of interleukin-12 production / phosphotyrosine residue binding / SH2 domain binding / Integrin signaling / FCERI mediated Ca+2 mobilization / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / B cell differentiation / FCGR3A-mediated IL10 synthesis / positive regulation of superoxide anion generation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / integrin-mediated signaling pathway / positive regulation of interleukin-8 production / calcium-mediated signaling / Regulation of signaling by CBL / positive regulation of protein-containing complex assembly / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / animal organ morphogenesis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / receptor internalization / Regulation of actin dynamics for phagocytic cup formation / platelet activation / CLEC7A (Dectin-1) signaling / positive regulation of interleukin-6 production / protein import into nucleus / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / positive regulation of tumor necrosis factor production
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 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 / 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
Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHobbs, H.T. / Badroos, J. / Gee, C.L. / Kuriyan, J.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Protein Sci. / Year: 2021
Title: Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases.
Authors: Hobbs, H.T. / Shah, N.H. / Badroos, J.M. / Gee, C.L. / Marqusee, S. / Kuriyan, J.
#1: Journal: Biorxiv / Year: 2021
Title: Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases
Authors: Hobbs, H.T. / Badroos, J. / Gee, C.L. / Marqusee, S. / Kuriyan, J.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 8, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase SYK
B: Tyrosine-protein kinase SYK
C: Tyrosine-protein kinase SYK
D: Tyrosine-protein kinase SYK
E: Tyrosine-protein kinase SYK
F: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)180,6736
Polymers180,6736
Non-polymers00
Water724
1
A: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)30,1121
Polymers30,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.882, 153.881, 85.472
Angle α, β, γ (deg.)90.00, 91.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Tyrosine-protein kinase SYK / / Spleen tyrosine kinase / p72-Syk


Mass: 30112.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P43405, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein- 35mg/mL in 10mM HEPES pH 7.0, 50mM NaCl, 5% glycerol and 1mM TCEP Crystal conditions-0.2M sodium nitrate and 10% w/v PEG 3350 Cryoprotectant-0.2M sodium nitrate, 20% PEG 3350, and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999816 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999816 Å / Relative weight: 1
ReflectionResolution: 3.2→45.78 Å / Num. obs: 30660 / % possible obs: 99.67 % / Redundancy: 8.3 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.3225 / Net I/σ(I): 7.47
Reflection shellResolution: 3.2→3.314 Å / Rmerge(I) obs: 2.097 / Num. unique obs: 3029 / CC1/2: 0.8417

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A81

1a81


Resolution: 3.2→45.78 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3039 1588 5.19 %
Rwork0.2697 --
obs0.2711 30598 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11296 0 0 4 11300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211560
X-RAY DIFFRACTIONf_angle_d0.66115609
X-RAY DIFFRACTIONf_dihedral_angle_d16.3064264
X-RAY DIFFRACTIONf_chiral_restr0.0441668
X-RAY DIFFRACTIONf_plane_restr0.0042025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.34081560.33722570X-RAY DIFFRACTION99
3.3-3.420.36311700.33472623X-RAY DIFFRACTION100
3.42-3.560.36551520.3522601X-RAY DIFFRACTION99
3.56-3.720.43111170.31432646X-RAY DIFFRACTION100
3.72-3.920.30631140.28732649X-RAY DIFFRACTION99
3.92-4.160.3331330.27432641X-RAY DIFFRACTION100
4.16-4.480.30421260.24872666X-RAY DIFFRACTION100
4.48-4.930.29271640.23352622X-RAY DIFFRACTION100
4.93-5.650.23861660.25062639X-RAY DIFFRACTION100
5.65-7.110.3011690.27462639X-RAY DIFFRACTION100
7.11-48.310.2631210.22952714X-RAY DIFFRACTION100

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