4XZ1

ZAP-70-tSH2:Compound-B adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding.

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.

(2015) Biochem J 465: 149-161

  • DOI: 10.1042/BJ20140793
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Zeta-chain associated protein of 70 kDa (ZAP-70) and spleen tyrosine kinase (Syk) are non-receptor tyrosine kinases that are essential for T-cell and B-cell antigen receptor signalling respectively. They are recruited, via their tandem-SH2 (Src-homol ...

    Zeta-chain associated protein of 70 kDa (ZAP-70) and spleen tyrosine kinase (Syk) are non-receptor tyrosine kinases that are essential for T-cell and B-cell antigen receptor signalling respectively. They are recruited, via their tandem-SH2 (Src-homology domain 2) domains, to doubly phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs) on invariant chains of immune antigen receptors. Because of their critical roles in immune signalling, ZAP-70 and Syk are targets for the development of drugs for autoimmune diseases. We show that three thiol-reactive small molecules can prevent the tandem-SH2 domains of ZAP-70 and Syk from binding to phosphorylated ITAMs. We identify a specific cysteine residue in the phosphotyrosine-binding pocket of each protein (Cys39 in ZAP-70, Cys206 in Syk) that is necessary for inhibition by two of these compounds. We also find that ITAM binding to ZAP-70 and Syk is sensitive to the presence of H2O2 and these two cysteine residues are also necessary for inhibition by H2O2. Our findings suggest a mechanism by which the reactive oxygen species generated during responses to antigen could attenuate signalling through these kinases and may also inform the development of ZAP-70 and Syk inhibitors that bind covalently to their SH2 domains.


    Organizational Affiliation

    *Department of Molecular and Cell Biology and Department of Chemistry, California Institute of Quantitative Biosciences and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, U.S.A.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
doubly phosphorylated ITAM peptide
B
21Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Find proteins for P20963 (Homo sapiens)
Go to UniProtKB:  P20963
NIH Common Fund Data Resources
PHAROS  P20963
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ZAP-70
A
262Homo sapiensMutation(s): 1 
Gene Names: ZAP70SRK
EC: 2.7.10.2
Find proteins for P43403 (Homo sapiens)
Go to UniProtKB:  P43403
NIH Common Fund Data Resources
PHAROS  P43403
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4N6
Query on 4N6

Download CCD File 
A
2-[(7-chloro-4-nitro-2,1,3-benzoxadiazol-5-yl)amino]ethanol
C8 H7 Cl N4 O4
NNUHMROEIBTAEX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.944α = 90
b = 61.105β = 116.37
c = 53.451γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States1RC2-AR058947-01

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence