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- PDB-6uib: Crystal structure of IL23 bound to peptide 23-652 -

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Basic information

Entry
Database: PDB / ID: 6uib
TitleCrystal structure of IL23 bound to peptide 23-652
Components
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
  • Peptide 23-652
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


late endosome lumen / regulation of tyrosine phosphorylation of STAT protein / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation / positive regulation of lymphocyte proliferation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...late endosome lumen / regulation of tyrosine phosphorylation of STAT protein / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation / positive regulation of lymphocyte proliferation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of tissue remodeling / positive regulation of activation of Janus kinase activity / tissue remodeling / sexual reproduction / positive regulation of T-helper 1 type immune response / positive regulation of NK T cell activation / positive regulation of smooth muscle cell apoptotic process / positive regulation of mononuclear cell proliferation / interleukin-12 receptor binding / positive regulation of memory T cell differentiation / natural killer cell activation / T-helper cell differentiation / positive regulation of osteoclast differentiation / Interleukin-23 signaling / negative regulation of interleukin-17 production / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Interleukin-12 signaling / response to UV-B / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / cytokine receptor activity / T-helper 1 type immune response / negative regulation of interleukin-10 production / cytokine binding / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / Interleukin-10 signaling / positive regulation of interleukin-10 production / positive regulation of cell adhesion / negative regulation of protein secretion / positive regulation of T-helper 17 cell lineage commitment / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / positive regulation of defense response to virus by host / regulation of cytokine production / positive regulation of interleukin-12 production / cytokine activity / negative regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of T cell mediated cytotoxicity / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell migration / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / defense response to virus / receptor complex / inflammatory response / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / 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 / Growth Hormone; Chain: A; ...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 / Immunoglobulins / Immunoglobulin-like fold / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsDurbin, J.D. / Wang, J. / Afshar, S.
CitationJournal: Plos One / Year: 2020
Title: Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage.
Authors: Pandya, P. / Sayers, R.O. / Ting, J.P. / Morshedian, S. / Torres, C. / Cudal, J.S. / Zhang, K. / Fitchett, J.R. / Zhang, Q. / Zhang, F.F. / Wang, J. / Durbin, J.D. / Carrillo, J.J. / Espada, ...Authors: Pandya, P. / Sayers, R.O. / Ting, J.P. / Morshedian, S. / Torres, C. / Cudal, J.S. / Zhang, K. / Fitchett, J.R. / Zhang, Q. / Zhang, F.F. / Wang, J. / Durbin, J.D. / Carrillo, J.J. / Espada, A. / Broughton, H. / Qian, Y. / Afshar, S.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
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_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-23 subunit alpha
B: Interleukin-12 subunit beta
C: Peptide 23-652
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8044
Polymers58,3793
Non-polymers4241
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-13 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.594, 94.665, 101.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interleukin-23 subunit alpha / IL-23-A / Interleukin-23 subunit p19 / IL-23p19


Mass: 19997.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NPF7
#2: 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: 36041.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29460
#3: Protein/peptide Peptide 23-652


Mass: 2340.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 100 mM Hepes pH 7, 17% w/v PEG 3350 and 150 mM Potassium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.74→101.133 Å / Num. all: 18723 / Num. obs: 18723 / % possible obs: 97.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 89.94 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Rsym value: 0.05 / Net I/av σ(I): 11.9 / Net I/σ(I): 23.9 / Num. measured all: 135345
Reflection shellResolution: 2.74→2.905 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3053 / Rpim(I) all: 0.181 / Rrim(I) all: 0.495 / Rsym value: 0.428 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DUH

3duh


Resolution: 2.74→19.9 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.428 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.424 / SU Rfree Blow DPI: 0.273 / SU Rfree Cruickshank DPI: 0.277
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1003 5.39 %RANDOM
Rwork0.206 ---
obs0.208 18625 97.5 %-
Displacement parametersBiso max: 193.07 Å2 / Biso mean: 84.89 Å2 / Biso min: 42.43 Å2
Baniso -1Baniso -2Baniso -3
1-8.2178 Å20 Å20 Å2
2--16.0397 Å20 Å2
3----24.2576 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.74→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 28 26 3234
Biso mean--89.78 63.86 -
Num. residues----421
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1048SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes477HARMONIC5
X-RAY DIFFRACTIONt_it3287HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion450SEMIHARMONIC5
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_contact3585SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3287HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4485HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion20.01
LS refinement shellResolution: 2.74→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.278 171 5.6 %
Rwork0.22 2882 -
all0.223 3053 -
obs--100 %
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)
12.55170.8035-1.31055.4442-1.27445.5175-0.0320.55920.1522-0.84030.00680.49880.243-0.16850.0252-0.13490.0462-0.107-0.1691-0.1316-0.2412-33.74924.0151-40.0396
27.89655.4110.1582.7453-1.18112.56550.03030.11180.76570.27920.0855-0.0303-0.4085-0.1938-0.1158-0.2157-0.1847-0.0324-0.260.0230.23324.203637.0264-17.5642
31.02380.89621.172200.543500.02130.006-0.0524-0.0577-0.009-0.01760.09780.0423-0.0124-0.0572-0.25280.03280.2485-0.08650.20382.52520.7323-27.6589
45.3043.94171.73854.60491.96922.59760.5357-0.089-0.15270.8507-0.5528-0.5453-0.17050.25020.01720.0667-0.1866-0.0577-0.14630.0416-0.1577-15.788916.3453-18.4332
51.10011.5285-0.7815.69-1.66392.4020.5656-0.3609-0.23720.8824-0.48190.1617-0.04760.1797-0.0837-0.0345-0.1323-0.0237-0.0734-0.0727-0.1396-32.1591-8.6429-15.6259
60.72880.4683-0.02510-0.444800.01140.0433-0.001-0.01540.0082-0.0244-0.01910.0114-0.0196-0.0545-0.304-0.00550.14520.13810.1224-6.929829.3331-27.2245
71.0284-1.5287-4.68832.3882-1.8424.37320.03830.2231-0.0922-0.4362-0.266-0.39140.57570.21620.22770.05490.0638-0.0312-0.0469-0.1046-0.0336-27.1873-8.9554-30.6282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A8 - 168
2X-RAY DIFFRACTION2{ B|0 - 86}B0 - 86
3X-RAY DIFFRACTION3{ B|87 - 91}B87 - 91
4X-RAY DIFFRACTION4{ B|92 - 211}B92 - 211
5X-RAY DIFFRACTION5{ B|212 - 312}B212 - 312
6X-RAY DIFFRACTION6{ B|313 - 314}B313 - 314
7X-RAY DIFFRACTION7{ C|* }C4 - 18

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