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- PDB-1a81: CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUN... -

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Basic information

Entry
Database: PDB / ID: 1a81
TitleCRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM
Components
  • SYK KINASE
  • T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
KeywordsCOMPLEX (TRANSFERASE/PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) / SYK / KINASE / SH2 DOMAIN / ITAM / COMPLEX (TRANSFERASE-PEPTIDE) complex
Function / homology
Function and homology information


gamma-delta T cell receptor complex / 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 / T cell anergy / Toll-like receptor binding ...gamma-delta T cell receptor complex / 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 / T cell anergy / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / serotonin secretion by platelet / positive regulation of cell-cell adhesion mediated by integrin / leukocyte activation involved in immune response / positive regulation of T cell anergy / neutrophil activation involved in immune response / lymph vessel development / positive regulation of mast cell degranulation / gamma-delta T cell differentiation / positive regulation of mast cell cytokine production / collagen-activated tyrosine kinase receptor signaling pathway / positive regulation of gamma-delta T cell differentiation / cell surface pattern recognition receptor signaling pathway / gamma-delta T cell activation / regulation of platelet activation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / cell activation / beta selection / cellular response to molecule of fungal origin / FLT3 signaling through SRC family kinases / positive regulation of CD4-positive, alpha-beta T cell proliferation / early phagosome / leukotriene biosynthetic process / alpha-beta T cell receptor complex / regulation of phagocytosis / positive thymic T cell selection / regulation of DNA-binding transcription factor activity / regulation of tumor necrosis factor-mediated signaling pathway / macrophage activation involved in immune response / interleukin-3-mediated signaling pathway / signal complex assembly / positive regulation of bone resorption / positive regulation of monocyte chemotactic protein-1 production / cellular response to lipid / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / positive regulation of cell adhesion mediated by integrin / positive regulation of B cell differentiation / positive regulation of cell-matrix adhesion / T cell receptor complex / leukocyte cell-cell adhesion / smoothened signaling pathway / mast cell degranulation / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / dendrite development / amyloid-beta clearance / alpha-beta T cell activation / positive regulation of interleukin-10 production / positive regulation of receptor internalization / Generation of second messenger molecules / FCGR activation / immunological synapse / cellular response to low-density lipoprotein particle stimulus / Co-inhibition by PD-1 / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of type I interferon production / Role of phospholipids in phagocytosis / phosphatase binding / regulation of ERK1 and ERK2 cascade / T cell receptor binding / phospholipase binding / GPVI-mediated activation cascade / Signaling by CSF3 (G-CSF) / positive regulation of superoxide anion generation / T cell costimulation / positive regulation of T cell proliferation / phosphotyrosine residue binding / neutrophil chemotaxis / Integrin signaling / positive regulation of interleukin-12 production / positive regulation of TORC1 signaling / positive regulation of interleukin-2 production / FCERI mediated Ca+2 mobilization / SH2 domain binding / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation
Similarity search - Function
Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / 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 / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. ...Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / 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 / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / SH2 domain / SHC Adaptor Protein / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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
T-cell surface glycoprotein CD3 epsilon chain / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsFuetterer, K. / Waksman, G.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structural basis for Syk tyrosine kinase ubiquity in signal transduction pathways revealed by the crystal structure of its regulatory SH2 domains bound to a dually phosphorylated ITAM peptide.
Authors: Futterer, K. / Wong, J. / Grucza, R.A. / Chan, A.C. / Waksman, G.
History
DepositionMar 31, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 25, 2016Group: Structure summary
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYK KINASE
B: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
C: SYK KINASE
D: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
E: SYK KINASE
F: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
G: SYK KINASE
H: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
I: SYK KINASE
J: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
K: SYK KINASE
L: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)186,69712
Polymers186,69712
Non-polymers00
Water00
1
G: SYK KINASE
H: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
I: SYK KINASE
J: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
K: SYK KINASE
L: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)93,3496
Polymers93,3496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: SYK KINASE
B: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
C: SYK KINASE
D: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN
E: SYK KINASE
F: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)93,3496
Polymers93,3496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SYK KINASE
D: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers31,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-15 kcal/mol
Surface area13840 Å2
MethodPISA
4
K: SYK KINASE
L: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers31,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-14 kcal/mol
Surface area12120 Å2
MethodPISA
5
G: SYK KINASE
H: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers31,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-13 kcal/mol
Surface area12300 Å2
MethodPISA
6
A: SYK KINASE
B: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers31,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-13 kcal/mol
Surface area13940 Å2
MethodPISA
7
I: SYK KINASE
J: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers31,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-12 kcal/mol
Surface area14060 Å2
MethodPISA
8
E: SYK KINASE
F: T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers31,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-14 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.500, 146.900, 91.500
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SYK KINASE


Mass: 28831.877 Da / Num. of mol.: 6 / Fragment: TANDEM SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P43405, EC: 2.7.1.112
#2: Protein/peptide
T-CELL SURFACE GLYCOPROTEIN CD3 EPSILON CHAIN / ITAM PEPTIDE


Mass: 2284.294 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07766
Has protein modificationY

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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: 3.05 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.5
Details: 10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117.5 mg/mlprotein1drop
24.5-6 %(w/v)PEG80001drop
35 %(v/v)PEG2001drop
40.05 MTris-HCl1drop
59-12 %(w/v)PEG80001reservoir
610 %(v/v)PEG2001reservoir
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 40670 / % possible obs: 89.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rsym value: 0.051
Reflection shellResolution: 3→3.07 Å / Redundancy: 3 % / Rsym value: 0.139 / % possible all: 74.1
Reflection
*PLUS
Num. measured all: 202021 / Rmerge(I) obs: 0.051

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MIR / Resolution: 3→30 Å / Rfactor Rfree error: 0.015 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.317 2000 5 %RANDOM
Rwork0.226 ---
obs0.226 40670 89.8 %-
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12201 0 0 0 12201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.378 226 -
Rwork0.308 4027 -
obs--76.3 %

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