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- PDB-4k2r: Structural basis for activation of ZAP-70 by phosphorylation of t... -

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Basic information

Entry
Database: PDB / ID: 4k2r
TitleStructural basis for activation of ZAP-70 by phosphorylation of the SH2-kinase linker
ComponentsTyrosine-protein kinase ZAP-70
KeywordsTRANSFERASE / kinase domain / SH2 domain / ATP Binding / cytoplam
Function / homology
Function and homology information


T cell aggregation / T cell migration / 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 / B cell activation ...T cell aggregation / T cell migration / 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 / B cell activation / Translocation of ZAP-70 to Immunological synapse / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / positive regulation of calcium-mediated signaling / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / T cell activation / calcium-mediated signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / cell-cell junction / T cell receptor signaling pathway / protein tyrosine kinase activity / adaptive immune response / cell differentiation / intracellular signal transduction / immune response / protein phosphorylation / signaling receptor binding / innate immune response / 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. / Src homology 2 domains ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / PHOSPHATE ION / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYan, Q. / Barros, T. / Visperas, P.R. / Deindl, S. / Kadlecek, T.A. / Weiss, A. / Kuriyan, J.
CitationJournal: Mol.Cell.Biol. / Year: 2013
Title: Structural Basis for Activation of ZAP-70 by Phosphorylation of the SH2-Kinase Linker.
Authors: Yan, Q. / Barros, T. / Visperas, P.R. / Deindl, S. / Kadlecek, T.A. / Weiss, A. / Kuriyan, J.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)70,1814
Polymers69,5561
Non-polymers6253
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.530, 53.150, 68.960
Angle α, β, γ (deg.)106.10, 93.26, 104.40
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 69555.891 Da / Num. of mol.: 1 / Mutation: D461N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAP70, SRK / Production host: Spodoptera frugiperda (fall armyworm)
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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1 M Bis-Tris pH 6.5, 20% Polyethylene glycol monomethyl ether 5,000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2012
RadiationMonochromator: KOHZU Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 12547 / Num. obs: 11992 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2 / Num. unique all: 1759 / % possible all: 94.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.09 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.827 / SU B: 55.031 / SU ML: 0.446 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28695 579 4.8 %RANDOM
Rwork0.20927 ---
obs0.21294 11374 93.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.923 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20.36 Å20.36 Å2
2--0.04 Å20.06 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 3→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 37 0 4435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194544
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9846141
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7835548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9423.333201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19615803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6981532
X-RAY DIFFRACTIONr_chiral_restr0.0880.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213422
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 51 -
Rwork0.328 835 -
obs--95.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6073-1.4620.61817.1417-1.09237.95640.3767-0.2589-0.5618-0.0498-0.03270.29290.2349-0.1225-0.3440.1524-0.0151-0.05030.0566-0.05170.1941-0.0917-2.482523.3524
23.5523-0.70221.14755.9814-1.28464.4126-0.03810.021-0.19250.1342-0.077-0.26140.18460.12370.11510.0630.0210.02190.04540.03810.15185.54993.682523.0775
31.9017-1.705-1.62893.58722.38322.75270.06260.13130.0079-0.2339-0.0520.2323-0.1165-0.299-0.01070.1102-0.02790.02540.21890.01950.0915-12.418810.76470.5866
414.41632.10743.35355.1897-2.70653.93940.19590.28091.02660.0788-0.12790.2233-0.34990.3418-0.0680.1377-0.01440.08480.1752-0.08590.1664-23.88621.451112.011
51.259-0.892-1.84112.11511.37392.7420.06790.19780.0369-0.2711-0.09520.0894-0.1305-0.25350.02730.06040.0333-0.06780.3162-0.03720.1691-13.88028.7172-0.4168
63.48461.2186-0.88559.5662-0.19594.1951-0.04180.1261-0.4827-0.3754-0.1519-0.61290.417-0.03290.19360.4517-0.0774-0.00840.34390.02540.09812.2249-7.5677-32.9716
70.67270.11830.59813.66680.96397.4008-0.02890.1033-0.2152-0.05530.0929-0.13220.35320.1025-0.0640.05260.03770.05860.08760.03070.13795.746-5.8274-16.3259
82.1697-3.07850.93555.8470.30682.56650.30960.35890.007-0.4426-0.2228-0.22760.64590.4901-0.08670.60050.04270.19810.21570.03810.464915.8265-16.0314-11.8865
94.7701-1.5206-0.76614.316-0.71151.6558-0.1566-0.6113-0.15430.24880.1126-0.59750.31010.37640.0440.36990.002-0.11470.16330.05620.307415.7553-12.5947-1.6503
1013.8604-26.3439-5.027750.549.34911.921.7030.85870.2074-2.3035-1.6646-0.433-1.02-0.3245-0.03841.96040.13190.00090.3616-0.07140.45648.938116.6969-4.4299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 114
3X-RAY DIFFRACTION3A115 - 174
4X-RAY DIFFRACTION4A175 - 220
5X-RAY DIFFRACTION5A221 - 327
6X-RAY DIFFRACTION6A328 - 386
7X-RAY DIFFRACTION7A387 - 479
8X-RAY DIFFRACTION8A480 - 538
9X-RAY DIFFRACTION9A539 - 606
10X-RAY DIFFRACTION10A607 - 614

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