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- PDB-2oq1: Tandem SH2 domains of ZAP-70 with 19-mer zeta1 peptide -

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Basic information

Entry
Database: PDB / ID: 2oq1
TitleTandem SH2 domains of ZAP-70 with 19-mer zeta1 peptide
Components
  • T-cell surface glycoprotein CD3 zeta chain
  • Tyrosine-protein kinase ZAP-70
KeywordsTRANSFERASE / tandem SH2 domains / ZAP-70 / tyrosine kinase
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 / Fc-gamma receptor signaling pathway / negative thymic T cell selection / 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 / Fc-gamma receptor signaling pathway / negative thymic T cell selection / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / protein complex oligomerization / B cell activation / alpha-beta T cell activation / RHOH GTPase cycle / Generation of second messenger molecules / T cell differentiation / FCGR activation / immunological synapse / Co-inhibition by PD-1 / Role of phospholipids in phagocytosis / T cell migration / Nuclear events stimulated by ALK signaling in cancer / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / T cell activation / protein tyrosine kinase binding / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / calcium-mediated signaling / peptidyl-tyrosine phosphorylation / Regulation of actin dynamics for phagocytic cup formation / 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 surface receptor signaling pathway / intracellular signal transduction / immune response / protein phosphorylation / protein heterodimerization activity / 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
LEAD (II) ION / T-cell surface glycoprotein CD3 zeta chain / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsHatada, M.H. / Laird, E.R. / Green, J. / Morgenstern, J. / Ram, M.K.
CitationJournal: Nature / Year: 1995
Title: Molecular basis for the interaction of ZAP-70 with the T-cell receptor
Authors: Hatada, M.H. / Lu, X. / Laird, E.R. / Green, J. / Morgenstern, J.P. / Lou, M. / Marr, C. / Phillips, T.B. / Ram, M.K. / Theriault, K.
History
DepositionJan 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN Cysteine 119 is modified with Trimethyl lead acetate. Carbons of methyls are missing from the model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ZAP-70
B: T-cell surface glycoprotein CD3 zeta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6293
Polymers31,4222
Non-polymers2071
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-13 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.110, 63.370, 54.000
Angle α, β, γ (deg.)90.00, 114.44, 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-associated protein / Syk-related tyrosine kinase


Mass: 28906.650 Da / Num. of mol.: 1 / Fragment: residues 3-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P43403, non-specific protein-tyrosine kinase
#2: Protein/peptide T-cell surface glycoprotein CD3 zeta chain / T-cell receptor T3 zeta chain / CD247 antigen


Mass: 2515.477 Da / Num. of mol.: 1 / Fragment: residues 69-87 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (Humans)
References: UniProt: P20963
#3: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20%PEG 4000, 50mM sodium citrate,100 mM ammonium acetate, 20mM DTT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: graphite monochromator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 23978 / Num. obs: 23978 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.049

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Processing

Software
NameVersionClassificationNB
X-PLOR3.843refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 2369 RANDOM
Rwork0.209 --
all0.209 23978 -
obs0.209 23697 -
Displacement parametersBiso mean: 20.989 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 1 342 2540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.58

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