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- PDB-5l04: STRUCTURE OF INTERFERON LAMBDA 1 RECEPTOR WITH HUMAN KINASE JAK1 -

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Basic information

Entry
Database: PDB / ID: 5l04
TitleSTRUCTURE OF INTERFERON LAMBDA 1 RECEPTOR WITH HUMAN KINASE JAK1
Components
  • Interferon lambda receptor 1
  • Tyrosine-protein kinase JAK1
Keywordstransferase/transferase inhibitor / COMPLEX OF JAK1 AND INTERFERON LAMBDA 1 / JAK KINASE / INTRACELLULAR DOMAIN OF IFNLR1 / FERM DOMAIN / SH2-LIKE DOMAIN / transferase-transferase inhibitor complex
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 / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion ...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 / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / 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 / Interleukin-2 signaling / growth hormone receptor binding / cytokine receptor activity / Other interleukin signaling / IFNG signaling activates MAPKs / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / type I interferon-mediated signaling pathway / Interleukin-6 signaling / 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 / Evasion by RSV of host interferon responses / 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 / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / defense response to virus / Potential therapeutics for SARS / cell differentiation / cytoskeleton / endosome / intracellular signal transduction / negative regulation of cell population proliferation / protein phosphorylation / response to antibiotic / 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
Tyrosine-protein kinase JAK1 / Interferon lambda receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLubkowski, J. / Wlodawer, A. / Zhang, D.
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Crystal Structure of a Complex of the Intracellular Domain of Interferon lambda Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1.
Authors: Zhang, D. / Wlodawer, A. / Lubkowski, J.
History
DepositionJul 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)69,4302
Polymers69,4302
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-26 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.700, 53.800, 87.390
Angle α, β, γ (deg.)90.000, 114.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 63977.047 Da / Num. of mol.: 1 / Fragment: unp residues 31-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK1, JAK1A, JAK1B / Plasmid: pET-32a(+) / Cell line (production host): Rosetta 2 (DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P23458, non-specific protein-tyrosine kinase
#2: Protein/peptide 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: 5453.267 Da / Num. of mol.: 1 / Fragment: unp residues 260-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNLR1, IL28RA, LICR2 / Plasmid: pET-32a(+) / Cell line (production host): Rosetta 2 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IU57
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.55 Å3/Da / Density % sol: 51.73 % / Description: thin planks (0.2 mm x 0.1 mm x 0.02 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7 mg/ml of protein in 50 mM Hepes buffer (pH 7.5) with 150 mM NaCl, mixesd with 1:1 ratio with 18% (w/v) PEG 3350, 0.2 M amonium formate
PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 40748 / % possible obs: 98.6 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.025 / Rrim(I) all: 0.081 / Χ2: 0.996 / Net I/av σ(I): 27.43 / Net I/σ(I): 7.8 / Num. measured all: 384056
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.1880.6340.89189.7
2.18-2.269.10.550.953196.2
2.26-2.379.20.4130.971199.9
2.37-2.499.50.3190.9831100
2.49-2.659.70.2290.991100
2.65-2.859.80.1650.9951100
2.85-3.149.90.1060.9971100
3.14-3.599.80.0780.9981100
3.59-4.529.60.060.9991100
4.52-999.40.050.998199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.96 Å
Translation2.5 Å24.96 Å

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Processing

Software
NameVersionClassification
SERGUIdata collection
SCALEPACKdata scaling
PHASER2.1.1phasing
REFMACrefinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→79.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.457 / SU ML: 0.12 / SU R Cruickshank DPI: 0.2227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.201
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1080 3.5 %RANDOM
Rwork0.1687 ---
obs0.1707 30056 75.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 179.19 Å2 / Biso mean: 50.996 Å2 / Biso min: 17.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-0.1 Å2
2--0.43 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2.1→79.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 0 185 4221
Biso mean---45.77 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194125
X-RAY DIFFRACTIONr_bond_other_d0.0040.023982
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9545568
X-RAY DIFFRACTIONr_angle_other_deg1.0673.0039059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71824200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30615745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.981526
X-RAY DIFFRACTIONr_chiral_restr0.1080.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.0214596
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02953
X-RAY DIFFRACTIONr_mcbond_it8.5529.0541981
X-RAY DIFFRACTIONr_mcbond_other8.5089.051980
X-RAY DIFFRACTIONr_mcangle_it10.50316.8252464
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 26 -
Rwork0.19 598 -
all-624 -
obs--20.55 %

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