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- PDB-7q63: The tandem SH2 domains of SYK -

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Basic information

Entry
Database: PDB / ID: 7q63
TitleThe tandem SH2 domains of SYK
ComponentsTyrosine-protein kinase SYK
KeywordsTRANSFERASE / Signalling / kinase
Function / homology
Function and homology information


interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / gamma-delta T cell differentiation / serotonin secretion by platelet / positive regulation of interleukin-3 production / positive regulation of gamma-delta T cell differentiation / B cell receptor complex ...interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / gamma-delta T cell differentiation / serotonin secretion by platelet / positive regulation of interleukin-3 production / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / neutrophil activation involved in immune response / positive regulation of mast cell cytokine production / lymph vessel development / regulation of platelet activation / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of mast cell degranulation / positive regulation of killing of cells of another organism / regulation of phagocytosis / beta selection / macrophage activation involved in immune response / early phagosome / cellular response to molecule of fungal origin / FLT3 signaling through SRC family kinases / leukotriene biosynthetic process / regulation of tumor necrosis factor-mediated signaling pathway / cellular response to lipid / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / regulation of DNA-binding transcription factor activity / positive regulation of cell adhesion mediated by integrin / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / blood vessel morphogenesis / positive regulation of alpha-beta T cell differentiation / 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 / positive regulation of interleukin-4 production / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / phospholipase binding / positive regulation of receptor internalization / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / FCGR activation / positive regulation of type I interferon production / phosphatase binding / positive regulation of bone resorption / 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 / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of interleukin-12 production / phosphotyrosine residue binding / Integrin signaling / SH2 domain binding / FCERI mediated Ca+2 mobilization / B cell differentiation / FCGR3A-mediated IL10 synthesis / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of interleukin-8 production / integrin-mediated signaling pathway / Regulation of signaling by CBL / calcium-mediated signaling / 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 / positive regulation of protein-containing complex assembly / Inactivation of CSF3 (G-CSF) signaling / receptor internalization / platelet activation / Regulation of actin dynamics for phagocytic cup formation / CLEC7A (Dectin-1) signaling / peptidyl-tyrosine phosphorylation / protein import into nucleus / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / DAP12 signaling
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
DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Chen, Z. / Bountra, C. / von Delft, F. / Gileadi, O. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: To Be Published
Title: The tandem SH2 domains of SYK
Authors: Bradshaw, W.J. / Katis, V.L. / Chen, Z. / Bountra, C. / von Delft, F. / Gileadi, O. / Brennan, P.E.
History
DepositionNov 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Tyrosine-protein kinase SYK
BBB: Tyrosine-protein kinase SYK
CCC: Tyrosine-protein kinase SYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,44715
Polymers89,7213
Non-polymers72612
Water5,837324
1
AAA: Tyrosine-protein kinase SYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2236
Polymers29,9071
Non-polymers3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Tyrosine-protein kinase SYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2016
Polymers29,9071
Non-polymers2945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Tyrosine-protein kinase SYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0233
Polymers29,9071
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.902, 152.580, 146.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11BBB-518-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53BBB
63CCC

NCS domain segments:

End auth comp-ID: GLY / End label comp-ID: GLY

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERAAAA5 - 2631 - 259
211SERSERBBBB5 - 2631 - 259
322ASNASNAAAA11 - 2637 - 259
422ASNASNCCCC11 - 2637 - 259
533ASNASNBBBB11 - 2637 - 259
633ASNASNCCCC11 - 2637 - 259

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Protein , 1 types, 3 molecules AAABBBCCC

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


Mass: 29906.971 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P43405, non-specific protein-tyrosine kinase

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Non-polymers , 5 types, 336 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM, potassium thiocyanate, 12.5% glycerol, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→146.82 Å / Num. obs: 76088 / % possible obs: 100 % / Redundancy: 26.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.043 / Rrim(I) all: 0.173 / Χ2: 0.82 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 24.7 % / Rmerge(I) obs: 4.548 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4468 / CC1/2: 0.559 / Rpim(I) all: 1.343 / Rrim(I) all: 4.744 / Χ2: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A81

1a81


Resolution: 1.9→76.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.598 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2643 1972 2.594 %
Rwork0.217 74051 -
all0.218 --
obs-76023 99.957 %
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: 52.278 Å2
Baniso -1Baniso -2Baniso -3
1--2.464 Å2-0 Å20 Å2
2---1.151 Å2-0 Å2
3---3.615 Å2
Refinement stepCycle: LAST / Resolution: 1.9→76.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5928 0 39 324 6291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155838
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6438342
X-RAY DIFFRACTIONr_angle_other_deg1.3011.58513482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0855766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.71722.047337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.321151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7071541
X-RAY DIFFRACTIONr_chiral_restr0.0690.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021455
X-RAY DIFFRACTIONr_nbd_refined0.2120.21173
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.25075
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22871
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.221
X-RAY DIFFRACTIONr_nbd_other0.2270.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.29
X-RAY DIFFRACTIONr_mcbond_it4.2515.2943037
X-RAY DIFFRACTIONr_mcbond_other4.2225.2893027
X-RAY DIFFRACTIONr_mcangle_it5.9127.9113788
X-RAY DIFFRACTIONr_mcangle_other5.9127.9123789
X-RAY DIFFRACTIONr_scbond_it4.5675.753157
X-RAY DIFFRACTIONr_scbond_other4.5665.7493158
X-RAY DIFFRACTIONr_scangle_it6.8538.4384547
X-RAY DIFFRACTIONr_scangle_other6.8528.4384548
X-RAY DIFFRACTIONr_lrange_it9.12761.5156760
X-RAY DIFFRACTIONr_lrange_other9.13561.4466718
X-RAY DIFFRACTIONr_ncsr_local_group_10.110.058125
X-RAY DIFFRACTIONr_ncsr_local_group_20.1290.056746
X-RAY DIFFRACTIONr_ncsr_local_group_30.1270.056790
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.109630.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.109630.05008
23AAAX-RAY DIFFRACTIONLocal ncs0.129350.05008
24CCCX-RAY DIFFRACTIONLocal ncs0.129350.05008
35BBBX-RAY DIFFRACTIONLocal ncs0.127250.05009
36CCCX-RAY DIFFRACTIONLocal ncs0.127250.05009
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
1.9-1.9490.4221500.39954220.455750.420.45599.94620.397
1.949-2.0030.3371210.35252780.35254000.5290.49599.98150.342
2.003-2.0610.3281220.31651410.31652690.6920.68599.88610.298
2.061-2.1240.3691360.29749930.29951360.7640.78699.86370.275
2.124-2.1940.3231380.26348690.26450100.8340.84299.94010.238
2.194-2.2710.3321360.27646630.27748020.7720.83199.93750.25
2.271-2.3560.3051300.25745150.25846460.8460.86999.97850.231
2.356-2.4520.2581190.21843740.21944930.8990.9131000.192
2.452-2.5610.2731270.21741610.21942900.9030.9299.95340.197
2.561-2.6860.2381280.20640150.20741430.9190.9271000.19
2.686-2.8310.278920.2238390.22139310.8940.9151000.205
2.831-3.0030.338960.24236160.24437120.8540.8971000.23
3.003-3.210.3151040.22933920.23134960.8650.9111000.225
3.21-3.4660.243730.22331950.22432680.930.931000.224
3.466-3.7960.236680.21329560.21330240.9330.9431000.22
3.796-4.2430.261580.18626860.18827440.9380.9481000.202
4.243-4.8970.184620.15823730.15824350.9660.9661000.179
4.897-5.9920.24680.18620110.18820790.9410.9581000.211
5.992-8.4470.235250.19816110.19916360.9590.9591000.224
8.447-76.290.229190.1989410.1999670.9580.95699.27610.227

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