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- PDB-4po6: Crystal structure of the human TYK2 FERM and SH2 domains with an ... -

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Basic information

Entry
Database: PDB / ID: 4po6
TitleCrystal structure of the human TYK2 FERM and SH2 domains with an IFNAR1 intracellular peptide
Components
  • Interferon alpha/beta receptor 1Interferon-alpha/beta receptor
  • Non-receptor tyrosine-protein kinase TYK2
KeywordsTRANSFERASE / FERM / SH2 / kinase / receptor / cytokine / intracellular
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response ...type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / growth hormone receptor binding / Other interleukin signaling / extrinsic component of plasma membrane / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / cytokine binding / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / positive regulation of natural killer cell proliferation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / growth hormone receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / positive regulation of T cell proliferation / non-specific protein-tyrosine kinase / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon alpha/beta signaling / positive regulation of type II interferon production / late endosome / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / response to lipopolysaccharide / cell differentiation / lysosome / cytoskeleton / intracellular signal transduction / immune response / protein phosphorylation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular exosome / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interferon alpha/beta receptor 1 / Tyrosine-protein kinase, non-receptor, TYK2, N-terminal / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain ...Interferon alpha/beta receptor 1 / Tyrosine-protein kinase, non-receptor, TYK2, N-terminal / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Interferon alpha/beta receptor 1 / Non-receptor tyrosine-protein kinase TYK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsWallweber, H.J.A. / Lupardus, P.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis of IFN receptor recognition by TYK2
Authors: Wallweber, H.J.A. / Tam, C. / Franke, Y. / Starovasnik, M.A. / Lupardus, P.J.
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-receptor tyrosine-protein kinase TYK2
B: Interferon alpha/beta receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7395
Polymers67,4632
Non-polymers2763
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-18 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.768, 52.422, 70.163
Angle α, β, γ (deg.)90.00, 108.09, 90.00
Int Tables number5
Space group name H-MC121
Detailssingle TYK2/IFNAR1 complex in assymetric unit

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Components

#1: Protein Non-receptor tyrosine-protein kinase TYK2


Mass: 63598.633 Da / Num. of mol.: 1 / Fragment: unp residues 23-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYK2 / Plasmid: pAC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P29597, non-specific protein-tyrosine kinase
#2: Protein/peptide Interferon alpha/beta receptor 1 / Interferon-alpha/beta receptor / IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor ...IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor family 2 member 1 / CRF2-1 / Type I interferon receptor 1


Mass: 3864.246 Da / Num. of mol.: 1 / Fragment: unp residues 475-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR, IFNAR1 / Plasmid: pAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17181
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 293 K / pH: 7
Details: 0.1 M Tris HCl pH 7.0, 0.2 M MgCl2, and 8-12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→38.55 Å / Num. obs: 42667 / % possible obs: 96.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.04 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.5
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.2 / % possible all: 92.2

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Processing

Software
NameVersionClassification
SSRLBLU-ICEdata collection
SOLVEphasing
BUSTER2.11.2refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: SAD MODEL

Resolution: 1.99→38.55 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2137 5.01 %RANDOM
Rwork0.199 ---
obs0.201 42641 95.6 %-
Displacement parametersBiso mean: 50.58 Å2
Baniso -1Baniso -2Baniso -3
1--5.4829 Å20 Å2-18.9011 Å2
2--5.551 Å20 Å2
3----0.0681 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: LAST / Resolution: 1.99→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 0 18 167 4140
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014093HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055549HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1397SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it4093HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion17.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4570SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3068 136 5.35 %
Rwork0.2729 2406 -
all0.2748 2542 -
obs--95.58 %

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