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- PDB-3qwr: Crystal structure of IL-23 in complex with an adnectin -

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Basic information

Entry
Database: PDB / ID: 3qwr
TitleCrystal structure of IL-23 in complex with an adnectin
Components
  • ADNECTIN
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
KeywordsPROTEIN BINDING/CYTOKINE / FOUR-HELIX BUNDLE CYTOKINE / IG DOMAIN / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / SECRETED / ANTIVIRAL DEFENSE / IMMUNE RESPONSE / INFLAMMATORY RESPONSE / INNATE IMMUNITY / TISSUE REMODELING / ADNECTIN / ENGINEERED BINDING PROTEIN / ANTIBODY MIMIC / PROTEIN BINDING-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 / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / response to UV-B / positive regulation of neutrophil chemotaxis / 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 / positive regulation of cell adhesion / regulation of cytokine production / 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: 3.25 Å
AuthorsWei, A. / Sheriff, S.
CitationJournal: Structure / Year: 2012
Title: Structures of adnectin/protein complexes reveal an expanded binding footprint.
Authors: Ramamurthy, V. / Krystek, S.R. / Bush, A. / Wei, A. / Emanuel, S.L. / Das Gupta, R. / Janjua, A. / Cheng, L. / Murdock, M. / Abramczyk, B. / Cohen, D. / Lin, Z. / Morin, P. / Davis, J.H. / ...Authors: Ramamurthy, V. / Krystek, S.R. / Bush, A. / Wei, A. / Emanuel, S.L. / Das Gupta, R. / Janjua, A. / Cheng, L. / Murdock, M. / Abramczyk, B. / Cohen, D. / Lin, Z. / Morin, P. / Davis, J.H. / Dabritz, M. / McLaughlin, D.C. / Russo, K.A. / Chao, G. / Wright, M.C. / Jenny, V.A. / Engle, L.J. / Furfine, E. / Sheriff, S.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 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-23 subunit alpha
D: ADNECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6654
Polymers65,9163
Non-polymers7491
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-6 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.700, 91.700, 225.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 34739.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Plasmid: PFBDUAL / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P29460
#2: Protein Interleukin-23 subunit alpha / IL-23 subunit alpha / IL-23-A / Interleukin-23 subunit p19 / IL-23p19


Mass: 18696.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Plasmid: PFBDUAL / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9NPF7
#3: Protein ADNECTIN


Mass: 12479.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET9 PCT734 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / pH: 7
Details: 0.1 M Tris-HCl, 1 M tri-sodium citrate, 0.2 M NaCl, pH 7.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→42.48 Å / Num. obs: 12835 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 85.75 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.6
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.13.0refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
AMoREphasing
BUSTER2.13.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IL-23 FROM UNPUBLISHED STRUCTURE AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509

1fnf


Resolution: 3.25→42.48 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.47
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1003 7.83 %RANDOM
Rwork0.234 ---
obs0.235 12815 97.7 %-
Displacement parametersBiso mean: 100.73 Å2
Baniso -1Baniso -2Baniso -3
1--16.6261 Å20 Å20 Å2
2---10.1829 Å20 Å2
3---26.809 Å2
Refine analyzeLuzzati coordinate error obs: 0.74 Å
Refinement stepCycle: LAST / Resolution: 3.25→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 50 1 4040
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014151HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.365684HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1321SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes604HARMONIC5
X-RAY DIFFRACTIONt_it4151HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion22.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion575SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4588SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.56 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 233 7.66 %
Rwork0.2306 2810 -
all0.2362 3043 -
obs--97.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.96280.367-0.83651.1726-0.15792.52970.0791-0.05480.06510.01720.0261-0.0039-0.28010.0804-0.10520.49590.0386-0.0572-0.3345-0.0253-0.40298.8537-41.3024-43.0592
23.7273-0.16961.20842.2769-0.64651.97970.0394-0.40290.20530.1645-0.0429-0.3459-0.03970.44310.00360.49310.0262-0.0993-0.0535-0.0483-0.419318.6541-41.1183-13.1264
32.56140.2341-2.10474.0379-0.07260.8634-0.03710.4725-0.077-0.17170.2310.7036-0.0058-0.3611-0.19390.4814-0.0418-0.0384-0.32580.0179-0.4189-10.0208-34.6959-28.6838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 305
2X-RAY DIFFRACTION2B7 - 168
3X-RAY DIFFRACTION3D3 - 93

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