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- PDB-3dlq: Crystal structure of the IL-22/IL-22R1 complex -

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Basic information

Entry
Database: PDB / ID: 3dlq
TitleCrystal structure of the IL-22/IL-22R1 complex
Components
  • Interleukin-22
  • Interleukin-22 receptor subunit alpha-1
KeywordsCYTOKINE/CYTOKINE RECEPTOR / cytokine-receptor complex / fibronectin-III / Cytokine / Glycoprotein / Polymorphism / Secreted / Membrane / Receptor / Transmembrane / CYTOKINE-CYTOKINE RECEPTOR COMPLEX
Function / homology
Function and homology information


interleukin-20 binding / interleukin-22 receptor binding / interferon receptor activity / interleukin-22 receptor activity / cytokine receptor activity / Interleukin-20 family signaling / response to glucocorticoid / cytokine activity / acute-phase response / cytokine-mediated signaling pathway ...interleukin-20 binding / interleukin-22 receptor binding / interferon receptor activity / interleukin-22 receptor activity / cytokine receptor activity / Interleukin-20 family signaling / response to glucocorticoid / cytokine activity / acute-phase response / cytokine-mediated signaling pathway / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / defense response to Gram-negative bacterium / inflammatory response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III ...Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-22 receptor subunit alpha-1 / Interleukin-22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBleicher, L. / de Moura, P.R. / Watanabe, L. / Colau, D. / Dumoutier, L. / Renauld, J.-C. / Polikarpov, I.
CitationJournal: Febs Lett. / Year: 2008
Title: Crystal structure of the IL-22/IL-22R1 complex and its implications for the IL-22 signaling mechanism
Authors: Bleicher, L. / de Moura, P.R. / Watanabe, L. / Colau, D. / Dumoutier, L. / Renauld, J.-C. / Polikarpov, I.
History
DepositionJun 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Interleukin-22
R: Interleukin-22 receptor subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)41,2782
Polymers41,2782
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-5 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.244, 79.244, 91.996
Angle α, β, γ (deg.)90.000, 94.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11R-260-

HOH

21R-261-

HOH

31R-397-

HOH

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Components

#1: Protein Interleukin-22 / IL-22 / IL-10-related T-cell-derived-inducible factor / IL-TIF


Mass: 17123.664 Da / Num. of mol.: 1 / Fragment: cytokine, UNP residues 29-179 / Mutation: C40A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL22 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q9GZX6
#2: Protein Interleukin-22 receptor subunit alpha-1 / IL-22R-alpha-1 / Cytokine receptor family 2 member 9 / CRF2-9


Mass: 24154.371 Da / Num. of mol.: 1 / Fragment: soluble portion, UNP residues 18-228 / Mutation: C204L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL22RA1 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q8N6P7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.17 Å3/Da / Density % sol: 43.24 % / Mosaicity: 0.877 °
Crystal growTemperature: 291 K / Method: hanging drop / pH: 7.5
Details: 0.9M Sodium Acetate, 1mM Triton X-100, 0.1M HEPES, pH 7.5, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2007
Details: Vertical Collimating Mirror, DCM, Toroidal Focusing Mirror
RadiationMonochromator: Double Flat Si(111) Crystal Monochromator with Fixed-exit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27404 / % possible obs: 98.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.106 / Χ2: 1.036 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.972.40.30525921.0694.8
1.97-2.052.70.25327461.03698.8
2.05-2.142.80.19327411.06399.1
2.14-2.252.80.17627241.0599
2.25-2.392.80.14727391.01299.4
2.39-2.582.80.13227671.02699.4
2.58-2.842.90.11227131.01898.8
2.84-3.252.90.10627811.03999.7
3.25-4.092.90.08927871.01100
4.09-502.90.09928141.05599.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1M4R, 1TFH

1m4r

1tfh


Resolution: 1.9→19.811 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.834 / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 1375 5.02 %RANDOM
Rwork0.1923 ---
all0.1946 27916 --
obs0.1946 27377 98.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.902 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso max: 116.35 Å2 / Biso mean: 30.241 Å2 / Biso min: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.258 Å20 Å20.449 Å2
2---0.187 Å20 Å2
3----0.071 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 0 309 2998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062739
X-RAY DIFFRACTIONf_angle_d1.0093696
X-RAY DIFFRACTIONf_chiral_restr0.068419
X-RAY DIFFRACTIONf_plane_restr0.004469
X-RAY DIFFRACTIONf_dihedral_angle_d15.1381023
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.897-1.9650.3171240.2422304242887
1.965-2.0440.251450.2042614275999
2.044-2.1360.2421490.1722607275699
2.136-2.2490.2351450.1742593273899
2.249-2.390.2961410.1822601274299
2.39-2.5740.2531300.1922656278699
2.574-2.8320.2331270.1852604273199
2.832-3.240.2341290.18226622791100
3.24-4.0770.1961280.17126902818100
4.077-19.8120.231570.2152671282899

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