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- PDB-3d85: Crystal structure of IL-23 in complex with neutralizing FAB -

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Basic information

Entry
Database: PDB / ID: 3d85
TitleCrystal structure of IL-23 in complex with neutralizing FAB
Components
  • (FAB of antibody 7G10, ...) x 2
  • Interleukin-12 subunit p40
  • Interleukin-23 subunit p19
KeywordsIMMUNE SYSTEM/CYTOKINE / Interleukin-23 / FAB / 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 / Fc-gamma receptor I complex 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 / complement-dependent cytotoxicity / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / Interleukin-12 signaling / IgG immunoglobulin complex / 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 / antibody-dependent cellular cytotoxicity / response to UV-B / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / T-helper 1 type immune response / Initial triggering of complement / 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 / FCGR activation / complement activation, classical pathway / negative regulation of protein secretion / Role of phospholipids in phagocytosis / cell surface receptor signaling pathway via JAK-STAT / positive regulation of T-helper 17 cell lineage commitment / T cell proliferation / antigen binding / 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 / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / cytokine activity / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / negative regulation of inflammatory response to antigenic stimulus / negative regulation of smooth muscle cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of actin dynamics for phagocytic cup formation / 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 / antibacterial humoral response / cell migration / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / blood microparticle / defense response to virus / adaptive immune response / 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 exosome / extracellular region / identical protein binding / membrane / plasma 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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
IMIDAZOLE / Immunoglobulin heavy constant gamma 1 / Interleukin-12 subunit beta / Interleukin-23 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBeyer, B.M. / Ingram, R. / Ramanathan, L. / Reichert, P. / Le, H. / Madison, V.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody
Authors: Beyer, B.M. / Ingram, R. / Ramanathan, L. / Reichert, P. / Le, H.V. / Madison, V. / Orth, P.
History
DepositionMay 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAB of antibody 7G10, light chain
B: FAB of antibody 7G10, heavy chain
C: Interleukin-23 subunit p19
D: Interleukin-12 subunit p40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0277
Polymers101,7224
Non-polymers3053
Water16,322906
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-63 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.386, 62.091, 107.261
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a hetero-tetramer with chains A and B representing the FAB, chain C is IL-23 subunit p19 and chain D is IL-23 subunit p40. One hetero-tetramer is located within the asymmetric unit.

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Interleukin-23 subunit p19 / Interleukin-23 subunit alpha / IL-23 subunit alpha / IL-23p19


Mass: 19669.137 Da / Num. of mol.: 1 / Fragment: subunit p19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798
Plasmid details: accordining to Invitrogen Bac-to-Bac manual
Plasmid: pFastBac Dual / Cell line (production host): Hi-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NPF7

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Antibody , 3 types, 3 molecules ABD

#1: Antibody FAB of antibody 7G10, light chain


Mass: 23454.979 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody FAB of antibody 7G10, heavy chain


Mass: 23843.705 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01857*PLUS
#4: Antibody Interleukin-12 subunit p40 / 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: 34753.973 Da / Num. of mol.: 1 / Fragment: subunit p40 / Mutation: N200Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2
Plasmid details: accordining to Invitrogen Bac-to-Bac manual
Plasmid: pFastBac Dual / Cell line (production host): Hi-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29460

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Non-polymers , 3 types, 909 molecules

#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 906 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MPD, 7% PEG 6000, 100mM Imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 24, 2005
RadiationMonochromator: cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→106.6 Å / Num. all: 77469 / Num. obs: 77159 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 30.449 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.1 / Num. unique all: 7636 / Rsym value: 0.466 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
BUSTER-TNT2.1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ngy

1ngy


Resolution: 1.9→106.6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 1541 2 %RANDOM
Rwork0.1713 ---
all0.1721 77469 --
obs0.1721 77149 99.02 %-
Displacement parametersBiso mean: 38.04 Å2
Baniso -1Baniso -2Baniso -3
1-5.258539 Å20 Å22.55984752 Å2
2---2.88611823 Å20 Å2
3----2.37242078 Å2
Refinement stepCycle: LAST / Resolution: 1.9→106.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 5 922 7509
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0167682
X-RAY DIFFRACTIONt_angle_deg1.25491602
X-RAY DIFFRACTIONt_dihedral_angle_d18.2212960
X-RAY DIFFRACTIONt_trig_c_planes0.0111522
X-RAY DIFFRACTIONt_gen_planes0.029685
X-RAY DIFFRACTIONt_it1.67676820
X-RAY DIFFRACTIONt_nbd0.0531045
LS refinement shellResolution: 1.9→2.01 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2462 225 1.87 %
Rwork0.2184 11839 -
all21.89 12064 -
obs--99.02 %

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