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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


interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / cellular response to lectin / B cell receptor complex / regulation of platelet aggregation / Toll-like receptor binding / serotonin secretion by platelet ...interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / 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 / neutrophil activation involved in immune response / lymph vessel development / gamma-delta T cell differentiation / positive regulation of mast cell degranulation / positive regulation of mast cell cytokine production / positive regulation of gamma-delta T cell differentiation / collagen-activated tyrosine kinase receptor signaling pathway / cell surface pattern recognition 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 / regulation of phagocytosis / leukotriene biosynthetic process / interleukin-3-mediated signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / macrophage activation involved in immune response / positive regulation of bone resorption / Fc epsilon receptor (FCERI) signaling / positive regulation of monocyte chemotactic protein-1 production / Interleukin-2 signaling / cellular response to lipid / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / positive regulation of cell adhesion mediated by integrin / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of B cell differentiation / T cell receptor complex / leukocyte cell-cell adhesion / Dectin-2 family / mast cell degranulation / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of interleukin-4 production / amyloid-beta clearance / FCGR activation / positive regulation of receptor internalization / positive regulation of interleukin-10 production / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / cellular response to low-density lipoprotein particle stimulus / regulation of ERK1 and ERK2 cascade / phosphatase binding / GPVI-mediated activation cascade / phospholipase binding / Signaling by CSF3 (G-CSF) / positive regulation of superoxide anion generation / peptidyl-tyrosine phosphorylation / Integrin signaling / positive regulation of type I interferon production / phosphotyrosine residue binding / neutrophil chemotaxis / positive regulation of interleukin-12 production / FCERI mediated Ca+2 mobilization / positive regulation of TORC1 signaling / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / SH2 domain binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell differentiation / animal organ morphogenesis / B cell receptor signaling pathway / positive regulation of interleukin-8 production / integrin-mediated signaling pathway / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / FCERI mediated MAPK activation / Regulation of signaling by CBL / apoptotic signaling pathway / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / calcium-mediated signaling / positive regulation of protein-containing complex assembly / platelet activation / Regulation of actin dynamics for phagocytic cup formation / receptor internalization / Inactivation of CSF3 (G-CSF) signaling / positive regulation of interleukin-6 production / integrin binding / CLEC7A (Dectin-1) signaling / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / protein import into nucleus / kinase activity
Similarity search - Function
Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / 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 / SHC Adaptor Protein / : / SH2 domain / Src homology 2 (SH2) domain profile. ...Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / 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 / SHC Adaptor Protein / : / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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

Downloads & links

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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


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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