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- PDB-4oli: The pseudokinase/kinase protein from JAK-family member TYK2 -

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Basic information

Entry
Database: PDB / ID: 4oli
TitleThe pseudokinase/kinase protein from JAK-family member TYK2
ComponentsNon-receptor tyrosine-protein kinase TYK2
KeywordsTRANSFERASE / protein kinase / phospho-transfer
Function / homology
Function and homology information


type III interferon-mediated signaling pathway / interleukin-10-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / Interleukin-12 signaling ...type III interferon-mediated signaling pathway / interleukin-10-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / Interleukin-12 signaling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / positive regulation of natural killer cell proliferation / growth hormone receptor binding / extrinsic component of plasma membrane / Other interleukin signaling / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / MAPK3 (ERK1) activation / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of interleukin-17 production / Interleukin-10 signaling / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / type II interferon-mediated signaling pathway / growth hormone receptor signaling pathway via JAK-STAT / Signaling by CSF3 (G-CSF) / positive regulation of T cell proliferation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of receptor signaling pathway via JAK-STAT / Inactivation of CSF3 (G-CSF) signaling / cellular response to virus / Evasion by RSV of host interferon responses / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / 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
Tyrosine-protein kinase, non-receptor, TYK2, N-terminal / 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 ...Tyrosine-protein kinase, non-receptor, TYK2, N-terminal / 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 / 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 / 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
Chem-2TT / Non-receptor tyrosine-protein kinase TYK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEigenbrot, C. / Ultsch, M. / Wallweber, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the pseudokinase-kinase domains from protein kinase TYK2 reveals a mechanism for Janus kinase (JAK) autoinhibition.
Authors: Lupardus, P.J. / Ultsch, M. / Wallweber, H. / Bir Kohli, P. / Johnson, A.R. / Eigenbrot, C.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-receptor tyrosine-protein kinase TYK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9363
Polymers73,3041
Non-polymers6322
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.015, 111.015, 123.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 73304.219 Da / Num. of mol.: 1 / Mutation: D1023N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P29597, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-2TT / 2-chloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide


Mass: 315.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14ClN3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE VARIANT, AS POSTED IN UNIPROT ENTRY P29597

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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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 15% PEG monomethylether 2000, HEPES pH 7.4 0.1 M, 1mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2009
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→46.09 Å / Num. all: 18450 / Num. obs: 18446 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 89.05 Å2 / Rsym value: 0.06 / Net I/σ(I): 21

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NYX

3nyx


Resolution: 2.8→46.09 Å / Cor.coef. Fo:Fc: 0.9382 / Cor.coef. Fo:Fc free: 0.8993 / SU R Cruickshank DPI: 1.272 / Isotropic thermal model: individual atom / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: 3 TLS groups
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 1077 5.84 %RANDOM
Rwork0.2014 ---
all0.205 18450 --
obs0.2046 18446 99.49 %-
Displacement parametersBiso mean: 83.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.4209 Å20 Å20 Å2
2---2.4209 Å20 Å2
3---4.8419 Å2
Refine analyzeLuzzati coordinate error obs: 0.464 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 44 8 4396
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014499HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.246092HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1552SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes651HARMONIC5
X-RAY DIFFRACTIONt_it4499HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion22.15
X-RAY DIFFRACTIONt_chiral_improper_torsion550SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5018SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3066 177 5.99 %
Rwork0.2393 2776 -
all0.2433 2953 -
obs--99.49 %
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)
12.6380.17990.34734.7424-0.37134.75420.06480.0025-0.4418-0.0222-0.0783-0.24450.54420.13860.0135-0.11260.04770.0176-0.21890.0061-0.304-35.665614.851238.8711
22.0142.2381-0.98622.4667-0.71144.92650.0971-0.0411-0.0253-0.4601-0.08550.1817-0.1584-0.1627-0.01160.2050.03830.0805-0.178-0.0677-0.207-38.409727.54420.8498
32.3135-2.1634-1.48432.1535-0.20594.9861-0.29810.0167-0.24590.54420.05190.29910.54420.15610.24620.304-0.13510.152-0.304-0.1045-0.2894-29.009614.0084-1.3262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|579 - A|858 A|1201 - A|1201 }A579 - 858
2X-RAY DIFFRACTION1{ A|579 - A|858 A|1201 - A|1201 }A1201
3X-RAY DIFFRACTION2{ A|859 - A|924 }A859 - 924
4X-RAY DIFFRACTION3{ A|925 - A|1177 A|1202 - A|1202 }A925 - 1177
5X-RAY DIFFRACTION3{ A|925 - A|1177 A|1202 - A|1202 }A1202

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