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- PDB-2ozo: Autoinhibited intact human ZAP-70 -

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Basic information

Entry
Database: PDB / ID: 2ozo
TitleAutoinhibited intact human ZAP-70
ComponentsTyrosine-protein kinase ZAP-70
KeywordsTRANSFERASE / Inactive ZAP-70 / tandem SH2 / Autoinhibition / ITAM / hydrogen bonding network / TCR signaling
Function / homology
Function and homology information


T cell aggregation / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / beta selection / positive thymic T cell selection / 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 / B cell activation ...T cell aggregation / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / beta selection / positive thymic T cell selection / 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 / B cell activation / RHOH GTPase cycle / Generation of second messenger molecules / T cell differentiation / immunological synapse / T cell migration / Nuclear events stimulated by ALK signaling in cancer / phosphotyrosine residue binding / positive regulation of calcium-mediated signaling / T cell activation / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / calcium-mediated signaling / peptidyl-tyrosine phosphorylation / cell-cell junction / T cell receptor signaling pathway / protein tyrosine kinase activity / adaptive immune response / intracellular signal transduction / immune response / protein phosphorylation / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / 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. ...Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDeindl, S. / Kadlecek, T.A. / Brdicka, T. / Cao, X. / Weiss, A. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structural Basis for the Inhibition of Tyrosine Kinase Activity of ZAP-70.
Authors: Deindl, S. / Kadlecek, T.A. / Brdicka, T. / Cao, X. / Weiss, A. / Kuriyan, J.
History
DepositionFeb 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ZAP-70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8793
Polymers69,3491
Non-polymers5312
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.297, 52.929, 69.331
Angle α, β, γ (deg.)105.91, 92.94, 103.72
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 69348.664 Da / Num. of mol.: 1 / Fragment: Inactive ZAP-70 (residues 1-606) / Mutation: Y315F,Y319F,D461N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAP70, SRK / Plasmid: pFastBac-1
Cell (production host): Baculovirus-infected insect cells Sf9
Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): TriEx Sf9
References: UniProt: P43403, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M NaSCN, 21% PEG3350, protein mixed with 9 mM n-decyl-beta-D-thiomaltopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.115879 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2006 / Details: Double crystal, Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 2.6→500 Å / Num. all: 19187 / Num. obs: 18285 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.089 / Net I/σ(I): 16.18
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.1 / Num. unique all: 1929 / Rsym value: 0.345 / % possible all: 78.5

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→500 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.29 1622 8.3 %
Rwork0.22 --
obs0.26 17302 88.3 %
all-19595 -
Solvent computationBsol: 38.888 Å2
Displacement parametersBiso mean: 42.418 Å2
Baniso -1Baniso -2Baniso -3
1--1.864 Å22.515 Å24.253 Å2
2--3.765 Å2-5.083 Å2
3----1.901 Å2
Refinement stepCycle: LAST / Resolution: 2.6→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 0 32 69 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3421.5
X-RAY DIFFRACTIONc_scbond_it1.7982
X-RAY DIFFRACTIONc_mcangle_it2.3052
X-RAY DIFFRACTIONc_scangle_it2.7692.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3ANP_par.txt
X-RAY DIFFRACTION4water_rep.param

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