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- PDB-4xz1: ZAP-70-tSH2:Compound-B adduct -

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Basic information

Entry
Database: PDB / ID: 4xz1
TitleZAP-70-tSH2:Compound-B adduct
Components
  • Tyrosine-protein kinase ZAP-70
  • doubly phosphorylated ITAM peptide
KeywordsTransferase/Transferase inhibitor / tyrosine kinase / cysteine adduct / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


T cell aggregation / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / positive regulation of alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / Fc-gamma receptor signaling pathway / beta selection / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface ...T cell aggregation / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / positive regulation of alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / Fc-gamma receptor signaling pathway / beta selection / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface / positive thymic T cell selection / Nef and signal transduction / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / T cell receptor complex / protein complex oligomerization / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / extrinsic component of cytoplasmic side of plasma membrane / B cell activation / alpha-beta T cell activation / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / FCGR activation / T cell differentiation / PD-1 signaling / Role of phospholipids in phagocytosis / T cell migration / Nuclear events stimulated by ALK signaling in cancer / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / protein tyrosine kinase binding / T cell activation / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / calcium-mediated signaling / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / cell-cell junction / Downstream TCR signaling / T cell receptor signaling pathway / protein-containing complex assembly / protein tyrosine kinase activity / adaptive immune response / cell differentiation / cell surface receptor signaling pathway / intracellular signal transduction / immune response / protein heterodimerization activity / protein phosphorylation / innate immune response / signaling receptor binding / Golgi apparatus / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 ...Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / 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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4N6 / T-cell surface glycoprotein CD3 zeta chain / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBarros, T. / Kuriyan, J. / Winger, J.A. / Visperas, P.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)1RC2-AR058947-01 United States
CitationJournal: Biochem. J. / Year: 2015
Title: Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding.
Authors: Visperas, P.R. / Winger, J.A. / Horton, T.M. / Shah, N.H. / Aum, D.J. / Tao, A. / Barros, T. / Yan, Q. / Wilson, C.G. / Arkin, M.R. / Weiss, A. / Kuriyan, J.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase ZAP-70
B: doubly phosphorylated ITAM peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4503
Polymers32,1912
Non-polymers2591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-15 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.944, 61.105, 53.451
Angle α, β, γ (deg.)90.00, 116.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase ZAP-70 / 70 kDa zeta-chain associated protein / Syk-related tyrosine kinase


Mass: 29515.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAP70, SRK / Production host: Escherichia coli (E. coli)
References: UniProt: P43403, non-specific protein-tyrosine kinase
#2: Protein/peptide doubly phosphorylated ITAM peptide


Mass: 2675.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P20963*PLUS
#3: Chemical ChemComp-4N6 / 2-[(7-chloro-4-nitro-2,1,3-benzoxadiazol-5-yl)amino]ethanol


Mass: 258.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7ClN4O4
Has protein modificationY
Nonpolymer detailsCompound B is 2-[(7-chloro-4-nitro-2,1,3-benzoxadiazol-5-yl)amino]ethanol. Atom CAL of 4N6 A 301 ...Compound B is 2-[(7-chloro-4-nitro-2,1,3-benzoxadiazol-5-yl)amino]ethanol. Atom CAL of 4N6 A 301 covalently linked to SG atom of CYS A 78 in this structure.

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 6000, calcium chloride, MES, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.989999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989999 Å / Relative weight: 1
ReflectionResolution: 2.8→47.89 Å / Num. obs: 7638 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OQ1

2oq1


Resolution: 2.8→47.89 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 370 4.85 %
Rwork0.2155 --
obs0.2181 7623 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 16 0 2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032251
X-RAY DIFFRACTIONf_angle_d0.6873050
X-RAY DIFFRACTIONf_dihedral_angle_d13.668844
X-RAY DIFFRACTIONf_chiral_restr0.027316
X-RAY DIFFRACTIONf_plane_restr0.003396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.20530.34871110.26232390X-RAY DIFFRACTION100
3.2053-4.0380.26021210.21422426X-RAY DIFFRACTION100
4.038-47.89650.25551380.20132437X-RAY DIFFRACTION100

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