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- PDB-5ixd: Structure of human JAK1 FERM/SH2 in complex with IFN lambda receptor -

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Basic information

Entry
Database: PDB / ID: 5ixd
TitleStructure of human JAK1 FERM/SH2 in complex with IFN lambda receptor
Components
  • Interferon lambda receptor 1
  • Tyrosine-protein kinase JAK1
KeywordsCYTOKINE / JAK kinase / JAK1 / IFNLR1 / interferon
Function / homology
Function and homology information


response to type III interferon / interleukin-28 receptor complex / mucosal immune response / protein localization to cell-cell junction / positive regulation of cellular respiration / interleukin-11-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / type III interferon-mediated signaling pathway ...response to type III interferon / interleukin-28 receptor complex / mucosal immune response / protein localization to cell-cell junction / positive regulation of cellular respiration / interleukin-11-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / type III interferon-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of defense response to virus by host / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / Interleukin-2 signaling / growth hormone receptor binding / Other interleukin signaling / IFNG signaling activates MAPKs / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / interleukin-6-mediated signaling pathway / positive regulation of sprouting angiogenesis / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Signaling by CSF3 (G-CSF) / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / ISG15 antiviral mechanism / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon gamma signaling / Interferon alpha/beta signaling / RAF/MAP kinase cascade / defense response to virus / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / cytoskeleton / endosome / intracellular signal transduction / negative regulation of cell population proliferation / response to antibiotic / protein phosphorylation / focal adhesion / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak1 / 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 central domain ...Tyrosine-protein kinase, non-receptor Jak1 / 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 central 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 (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 / 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
CITRIC ACID / Tyrosine-protein kinase JAK1 / Interferon lambda receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsFerrao, R. / Wallweber, H.J.A. / Lupardus, P.J.
CitationJournal: Structure / Year: 2016
Title: The Structural Basis for Class II Cytokine Receptor Recognition by JAK1.
Authors: Ferrao, R. / Wallweber, H.J. / Ho, H. / Tam, C. / Franke, Y. / Quinn, J. / Lupardus, P.J.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Data collection
Revision 1.3Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK1
B: Interferon lambda receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6913
Polymers69,4992
Non-polymers1921
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-13 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.170, 193.200, 72.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tyrosine-protein kinase JAK1 / Janus kinase 1 / JAK-1


Mass: 63362.254 Da / Num. of mol.: 1 / Fragment: UNP residues 35-559
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK1, JAK1A, JAK1B / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P23458, non-specific protein-tyrosine kinase
#2: Protein Interferon lambda receptor 1 / IFN-lambda-R1 / Cytokine receptor class-II member 12 / Cytokine receptor family 2 member 12 / CRF2- ...IFN-lambda-R1 / Cytokine receptor class-II member 12 / Cytokine receptor family 2 member 12 / CRF2-12 / Interleukin-28 receptor subunit alpha / IL-28RA / Likely interleukin or cytokine receptor 2 / LICR2


Mass: 6136.950 Da / Num. of mol.: 1 / Fragment: UNP residues 250-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNLR1, IL28RA, LICR2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IU57
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7

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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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1-0.2 M Ammonium Citrate tribasic pH 7, 5-15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→44.29 Å / Num. obs: 18724 / % possible obs: 99.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 80.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.1
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PO6

4po6


Resolution: 2.85→44.29 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.73
RfactorNum. reflection% reflection
Rfree0.2823 1866 9.97 %
Rwork0.2488 --
obs0.2521 18707 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.85→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 13 0 3466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063546
X-RAY DIFFRACTIONf_angle_d1.0414817
X-RAY DIFFRACTIONf_dihedral_angle_d19.8491247
X-RAY DIFFRACTIONf_chiral_restr0.32542
X-RAY DIFFRACTIONf_plane_restr0.003610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8482-2.92520.45441380.39781284X-RAY DIFFRACTION99
2.9252-3.01130.35751440.34251291X-RAY DIFFRACTION100
3.0113-3.10850.3961450.31281262X-RAY DIFFRACTION100
3.1085-3.21950.34641390.31276X-RAY DIFFRACTION100
3.2195-3.34840.33121390.2981285X-RAY DIFFRACTION100
3.3484-3.50070.29041410.27411310X-RAY DIFFRACTION100
3.5007-3.68520.27621460.25151266X-RAY DIFFRACTION100
3.6852-3.9160.27991420.23811284X-RAY DIFFRACTION99
3.916-4.21810.25761390.22471283X-RAY DIFFRACTION98
4.2181-4.64220.22571460.20861298X-RAY DIFFRACTION99
4.6422-5.3130.25511460.19571314X-RAY DIFFRACTION100
5.313-6.69010.28081450.25611320X-RAY DIFFRACTION99
6.6901-44.29530.28091560.25211368X-RAY DIFFRACTION98
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)
14.105-0.8286-1.61631.5376-0.09492.281-0.8820.4416-0.6323-0.36320.05580.14830.9087-0.64020.04180.6935-0.3020.3610.8165-0.15420.727613.737227.4634-0.5202
26.25112.4044-1.53695.2732-1.0255.0931-0.36970.25630.1092-0.2358-0.07910.01710.2399-0.06510.33010.3031-0.0150.11240.71940.00860.771533.398843.5911-12.0087
30.8322-0.090.15261.3340.26880.5675-0.47470.0382-0.5263-0.524-0.1065-0.78860.76590.43270.09421.17870.0680.72490.9288-0.10051.093937.709217.1188-14.1637
48.0512-3.4453-5.77195.05010.6745.04010.18180.5824-0.5080.19380.472-0.3414-0.37620.632-0.34060.37180.18620.03971.09570.20220.7015-6.764351.98219.4105
52.21480.8416-0.52140.97040.31851.14-0.12310.9821-0.7163-0.2429-0.39870.12510.0682-0.2096-0.20070.34620.02270.04111.49670.02530.9486-5.624442.6284-0.4414
68.3824-2.18291.24979.61885.81069.9965-0.3331-0.36760.1915-1.42630.7137-0.1259-2.0105-0.6118-0.1770.871-0.24990.11321.138-0.46640.7946-0.698231.2815-10.5118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 277 )
2X-RAY DIFFRACTION2chain 'A' and (resid 278 through 386 )
3X-RAY DIFFRACTION3chain 'A' and (resid 387 through 558 )
4X-RAY DIFFRACTION4chain 'B' and (resid 250 through 255 )
5X-RAY DIFFRACTION5chain 'B' and (resid 256 through 264 )
6X-RAY DIFFRACTION6chain 'B' and (resid 265 through 270 )

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