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- PDB-3duh: Structure of Interleukin-23 -

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Basic information

Entry
Database: PDB / ID: 3duh
TitleStructure of Interleukin-23
Components
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
KeywordsIMMUNE SYSTEM/CYTOKINE / four-helix bundle cytokine / Ig domain / Cytokine / Glycoprotein / Immunoglobulin domain / Secreted / Antiviral defense / Immune response / Inflammatory response / Innate immunity / Tissue remodeling / IMMUNE SYSTEM / IMMUNE SYSTEM-CYTOKINE COMPLEX
Function / homology
Function and homology information


late endosome lumen / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / negative regulation of vascular endothelial growth factor signaling pathway / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...late endosome lumen / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / negative regulation of vascular endothelial growth factor signaling pathway / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lymphocyte proliferation / positive regulation of tissue remodeling / tissue remodeling / positive regulation of smooth muscle cell apoptotic process / positive regulation of NK T cell activation / positive regulation of T-helper 1 type immune response / sexual reproduction / positive regulation of mononuclear cell proliferation / interleukin-12 receptor binding / T-helper cell differentiation / positive regulation of memory T cell differentiation / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / positive regulation of NK T cell proliferation / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / Interleukin-12 signaling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / positive regulation of neutrophil chemotaxis / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / response to UV-B / T-helper 1 type immune response / negative regulation of interleukin-10 production / defense response to protozoan / Interleukin-10 signaling / positive regulation of interleukin-17 production / positive regulation of natural killer cell proliferation / positive regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of protein secretion / cell surface receptor signaling pathway via JAK-STAT / positive regulation of T-helper 17 cell lineage commitment / T cell proliferation / positive regulation of defense response to virus by host / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / regulation of cytokine production / positive regulation of cell adhesion / cytokine activity / negative regulation of inflammatory response to antigenic stimulus / negative regulation of smooth muscle cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to type II interferon / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / defense response to virus / endoplasmic reticulum lumen / inflammatory response / protein heterodimerization activity / innate immune response / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane / cytosol
Similarity search - Function
Interleukin-23 alpha / Interleukin 23 subunit alpha / Interleukin-12 beta / Interleukin-12 beta, central domain / : / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core ...Interleukin-23 alpha / Interleukin 23 subunit alpha / Interleukin-12 beta / Interleukin-12 beta, central domain / : / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-12 subunit beta / Interleukin-23 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLupardus, P.J. / Garcia, K.C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The structure of interleukin-23 reveals the molecular basis of p40 subunit sharing with interleukin-12.
Authors: Lupardus, P.J. / Garcia, K.C.
History
DepositionJul 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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-12 subunit beta
B: Interleukin-12 subunit beta
C: Interleukin-23 subunit alpha
D: Interleukin-23 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3416
Polymers110,8994
Non-polymers4422
Water3,603200
1
A: Interleukin-12 subunit beta
C: Interleukin-23 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6703
Polymers55,4492
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-5 kcal/mol
Surface area23760 Å2
MethodPISA
2
B: Interleukin-12 subunit beta
D: Interleukin-23 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6703
Polymers55,4492
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-6 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.089, 59.974, 160.365
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Interleukin-12 subunit beta / IL-12B / IL-12 subunit p40 / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / NK ...IL-12B / IL-12 subunit p40 / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / NK cell stimulatory factor chain 2 / NKSF2


Mass: 35811.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Plasmid: pACSG2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HiFive / References: UniProt: P29460
#2: Protein Interleukin-23 subunit alpha / IL-23 subunit alpha / Interleukin-23 subunit p19 / IL-23p19


Mass: 19638.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Plasmid: pACSG2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HiFive / References: UniProt: Q9NPF7
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2M potassium nitrate, 0.1M Hepes-NaOH pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 4, 2008
RadiationMonochromator: Si(111), Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 49424 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.5 / Num. unique all: 7208 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human p40 from PDB ID 1F45

1f45


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.997 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26833 2502 5.1 %RANDOM
Rwork0.22794 ---
obs0.23007 46921 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.587 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å22.55 Å2
2---0.13 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 28 200 7010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226977
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9489500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60324.342304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.813151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2121532
X-RAY DIFFRACTIONr_chiral_restr0.0930.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025266
X-RAY DIFFRACTIONr_nbd_refined0.2030.22732
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.2130
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.220
X-RAY DIFFRACTIONr_mcbond_it0.9351.54416
X-RAY DIFFRACTIONr_mcangle_it1.60926958
X-RAY DIFFRACTIONr_scbond_it1.70832962
X-RAY DIFFRACTIONr_scangle_it2.6414.52542
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 189 -
Rwork0.282 3425 -
obs--100 %

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