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- PDB-3g9v: Crystal structure of a soluble decoy receptor IL-22BP bound to in... -

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Basic information

Entry
Database: PDB / ID: 3g9v
TitleCrystal structure of a soluble decoy receptor IL-22BP bound to interleukin-22
Components
  • Interleukin 22 receptor, alpha 2
  • Interleukin-22
KeywordsCYTOKINE/CYTOKINE RECEPTOR / CYTOKINE / CYTOKINE RECEPTOR / Receptor / Glycoprotein / Polymorphism / Secreted / CYTOKINE-CYTOKINE RECEPTOR COMPLEX
Function / homology
Function and homology information


interleukin-22 binding / interleukin-22 receptor activity / interleukin-22 receptor binding / cytokine receptor activity / Interleukin-20 family signaling / response to glucocorticoid / cytokine activity / acute-phase response / negative regulation of inflammatory response / cytokine-mediated signaling pathway ...interleukin-22 binding / interleukin-22 receptor activity / interleukin-22 receptor binding / cytokine receptor activity / Interleukin-20 family signaling / response to glucocorticoid / cytokine activity / acute-phase response / negative regulation of inflammatory response / cytokine-mediated signaling pathway / Signaling by ALK fusions and activated point mutants / inflammatory response / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core ...Interleukin-22 / Interleukin 22 IL-10-related T-cell-derived-inducible factor / Interleukin-10, conserved site / Interleukin-10 family signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-22 receptor subunit alpha-2 / Interleukin-22 receptor subunit alpha-2 / Interleukin-22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.756 Å
Authorsde Moura, P.R. / Watanabe, L. / Bleicher, L. / Colau, D. / Renauld, J.-C. / Polikarpov, I.
CitationJournal: FEBS Lett. / Year: 2009
Title: Crystal structure of a soluble decoy receptor IL-22BP bound to interleukin-22
Authors: de Moura, P.R. / Watanabe, L. / Bleicher, L. / Colau, D. / Dumoutier, L. / Lemaire, M.M. / Renauld, J.-C. / Polikarpov, I.
History
DepositionFeb 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin 22 receptor, alpha 2
B: Interleukin-22
C: Interleukin 22 receptor, alpha 2
D: Interleukin-22


Theoretical massNumber of molelcules
Total (without water)83,8434
Polymers83,8434
Non-polymers00
Water3,009167
1
A: Interleukin 22 receptor, alpha 2
B: Interleukin-22


Theoretical massNumber of molelcules
Total (without water)41,9212
Polymers41,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-4 kcal/mol
Surface area15190 Å2
MethodPISA
2
C: Interleukin 22 receptor, alpha 2
D: Interleukin-22


Theoretical massNumber of molelcules
Total (without water)41,9212
Polymers41,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-4 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.948, 67.948, 172.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 29:52 or resseq 56:136 or resseq...
21chain C and (resseq 29:52 or resseq 56:136 or resseq...
12chain B and (resseq 41:130 or resseq 140:178 )
22chain D and (resseq 41:130 or resseq 140:178 )

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUALAALAAA29 - 529 - 32
121ASNASNTHRTHRAA56 - 13636 - 116
131LEULEUASNASNAA142 - 160122 - 140
141SERSERILEILEAA162 - 176142 - 156
151GLUGLUGLUGLUAA183 - 195163 - 175
161CYSCYSSERSERAA206 - 223186 - 203
211LEULEUALAALACC29 - 529 - 32
221ASNASNTHRTHRCC56 - 13636 - 116
231LEULEUASNASNCC142 - 160122 - 140
241SERSERILEILECC162 - 176142 - 156
251GLUGLUGLUGLUCC183 - 195163 - 175
261CYSCYSSERSERCC206 - 223186 - 203
112ARGARGSERSERBB41 - 13013 - 102
122HISHISCYSCYSBB140 - 178112 - 150
212ARGARGSERSERDD41 - 13013 - 102
222HISHISCYSCYSDD140 - 178112 - 150

NCS ensembles :
ID
1
2

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Components

#1: Protein Interleukin 22 receptor, alpha 2 / INTERLEUKIN-22 BINDING PROTEIN / isoform CRA_a


Mass: 24765.707 Da / Num. of mol.: 2 / Fragment: UNP residues 21-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL22RA2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q08AH7, UniProt: Q969J5*PLUS
#2: Protein Interleukin-22 / IL-22 / IL-10-related T-cell-derived-inducible factor / IL-TIF


Mass: 17155.730 Da / Num. of mol.: 2 / Fragment: UNP residues 29-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL22 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9GZX6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 25mM Bicine, 150mM NaCl, 1mM CHAPS, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.43 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2008
RadiationMonochromator: Two Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 20212 / Num. obs: 19525 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 41.39 Å2 / Rsym value: 0.126 / Net I/σ(I): 1.61
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.61 / Num. unique all: 1987 / Rsym value: 0.5 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLQ

3dlq


Resolution: 2.756→24.842 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.81 / SU ML: 0.08 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.282 993 5.11 %RANDOM
Rwork0.213 18445 --
obs0.216 19438 96.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.102 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 39.83 Å2 / Biso min: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.444 Å20 Å20 Å2
2--0.444 Å2-0 Å2
3----0.888 Å2
Refinement stepCycle: LAST / Resolution: 2.756→24.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 0 167 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095210
X-RAY DIFFRACTIONf_angle_d1.2337025
X-RAY DIFFRACTIONf_chiral_restr0.088744
X-RAY DIFFRACTIONf_plane_restr0.005907
X-RAY DIFFRACTIONf_dihedral_angle_d18.7371941
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1433X-RAY DIFFRACTIONPOSITIONAL
12C1433X-RAY DIFFRACTIONPOSITIONAL0.05
21B1044X-RAY DIFFRACTIONPOSITIONAL
22D1044X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7558-2.90090.34041560.22772679X-RAY DIFFRACTION98
2.9009-3.08240.31261310.22252701X-RAY DIFFRACTION99
3.0824-3.31990.29411480.21162670X-RAY DIFFRACTION99
3.3199-3.6530.28951510.18582669X-RAY DIFFRACTION98
3.653-4.17940.23171540.1832616X-RAY DIFFRACTION96
4.1794-5.25740.23421400.17072602X-RAY DIFFRACTION95
5.2574-24.84260.31521130.2482508X-RAY DIFFRACTION90

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