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- PDB-3dgc: Structure of IL-22/IL-22R1 -

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Basic information

Entry
Database: PDB / ID: 3dgc
TitleStructure of IL-22/IL-22R1
Components
  • Interleukin-22
  • Interleukin-22 receptor subunit alpha-1
Keywordscytokine/signaling protein / IL-22 / IL-22R1 / cytokine / receptor / signaling molecule / Glycoprotein / Secreted / Membrane / Transmembrane / cytokine-signaling protein 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 / membrane => GO:0016020 / 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
ACETATE ION / URANYL (VI) ION / URANIUM ATOM / Interleukin-22 receptor subunit alpha-1 / Interleukin-22 / Interleukin-22 receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJones, B.C. / Logsdon, N.J. / Walter, M.R.
CitationJournal: Structure / Year: 2008
Title: Structure of IL-22 Bound to Its High-Affinity IL-22R1 Chain.
Authors: Jones, B.C. / Logsdon, N.J. / Walter, M.R.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Interleukin-22
R: Interleukin-22 receptor subunit alpha-1
M: Interleukin-22
S: Interleukin-22 receptor subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,61022
Polymers80,6024
Non-polymers4,00818
Water2,954164
1
L: Interleukin-22
R: Interleukin-22 receptor subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,65910
Polymers40,3012
Non-polymers2,3588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Interleukin-22
S: Interleukin-22 receptor subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,95012
Polymers40,3012
Non-polymers1,64910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.509, 75.480, 101.140
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules LMRS

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


Mass: 16343.888 Da / Num. of mol.: 2 / Fragment: UNP residues 39-179 / Mutation: N68Q, N97Q / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9GZX6
#2: Protein Interleukin-22 receptor subunit alpha-1 / IL-22R-alpha-1 / Cytokine receptor family 2 member 9 / CRF2-9


Mass: 23957.113 Da / Num. of mol.: 2 / Fragment: UNP residues 19-225 / Mutation: N62D, N69D, T71Q / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HB22, UniProt: Q8N6P7*PLUS

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Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 181 molecules

#4: Chemical
ChemComp-U1 / URANIUM ATOM


Mass: 238.029 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: U
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2U
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorDate: Dec 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 27346 / % possible obs: 96.4 % / Redundancy: 7 % / Biso Wilson estimate: 41.3 Å2 / Rsym value: 0.071

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å
RfactorNum. reflection
Rfree0.27 1367
Rwork0.222 -
obs-25664
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 85 164 5818

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