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- PDB-5mxa: Structure of unbound Interleukin-23 -

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Basic information

Entry
Database: PDB / ID: 5mxa
TitleStructure of unbound Interleukin-23
Components
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
KeywordsCYTOKINE / extracellular / inflammation / Fibronectin type III
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
VLAIO Belgium
Citation
Journal: Immunity / Year: 2018
Title: Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12R beta 1.
Authors: Bloch, Y. / Bouchareychas, L. / Merceron, R. / Skladanowska, K. / Van den Bossche, L. / Detry, S. / Govindarajan, S. / Elewaut, D. / Haerynck, F. / Dullaers, M. / Adamopoulos, I.E. / Savvides, S.N.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Preparation, crystallization and preliminary X-ray diffraction studies of the glycosylated form of human interleukin-23.
Authors: Shirouzono, T. / Chirifu, M. / Nakamura, C. / Yamagata, Y. / Ikemizu, S.
History
DepositionJan 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Feb 7, 2018Group: Structure summary / Category: entity / Item: _entity.details
Revision 1.5Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / 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 / _chem_comp.name / _chem_comp.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.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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,8283
Polymers59,0792
Non-polymers7491
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint1 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.849, 109.849, 87.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 21865.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The native secretion signal is likely cleaved off between residues 27 and 28
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Plasmid: pCDNA4/TO / Details (production host): stable cell line / Cell line (production host): HEK293S MGAT1-/- TetR / Production host: Homo sapiens (human) / 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: 37212.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The native secretion signal is likely cleaved off between residues 22 and 23
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Plasmid: pCDNA4/TO / Details (production host): stable cell line / Cell line (production host): HEK293S MGAT1-/- TetR / Production host: Homo sapiens (human) / References: UniProt: P29460
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.16 % / Description: single, dipyramidal
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 100 mM citrate, 100 mM sodium phosphate, 20.5 % PEG 1000, 200 mM lithium sulphate
Temp details: Molecular Dimensions cooled crystallisation incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→87.69 Å / Num. obs: 20825 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.27 % / Biso Wilson estimate: 69.45 Å2 / CC1/2: 1 / Rrim(I) all: 0.066 / Net I/σ(I): 24.59
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 10.14 % / Mean I/σ(I) obs: 2.24 / Num. unique obs: 3297 / CC1/2: 0.731 / Rrim(I) all: 1.031 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDS20161205data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IL-23 from pdb 4OE8

4oe8
PDB Unreleased entry


Resolution: 2.501→64.495 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.76
RfactorNum. reflection% reflection
Rfree0.2287 1716 8.24 %
Rwork0.1881 --
obs0.1914 20823 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→64.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 50 36 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033539
X-RAY DIFFRACTIONf_angle_d0.734831
X-RAY DIFFRACTIONf_dihedral_angle_d13.7492121
X-RAY DIFFRACTIONf_chiral_restr0.044557
X-RAY DIFFRACTIONf_plane_restr0.004608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5014-2.5750.37391340.29661543X-RAY DIFFRACTION97
2.575-2.65810.29091450.25851592X-RAY DIFFRACTION100
2.6581-2.75310.30641360.24651591X-RAY DIFFRACTION100
2.7531-2.86330.26741390.24581571X-RAY DIFFRACTION100
2.8633-2.99360.30231460.24031602X-RAY DIFFRACTION100
2.9936-3.15150.30741390.23061590X-RAY DIFFRACTION100
3.1515-3.34890.26141410.20551597X-RAY DIFFRACTION100
3.3489-3.60740.25761480.19651584X-RAY DIFFRACTION100
3.6074-3.97040.20741430.17591595X-RAY DIFFRACTION100
3.9704-4.54480.17611490.15071609X-RAY DIFFRACTION100
4.5448-5.72550.1771430.14811602X-RAY DIFFRACTION100
5.7255-64.51610.23151530.18941631X-RAY DIFFRACTION100
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)
14.0677-1.92893.73093.75980.39085.01920.0453-0.1727-1.2120.02080.3620.67260.15-0.041-0.36350.6006-0.0212-0.10340.57990.15670.628234.3248-63.735110.8684
24.3873-2.72440.08642.67950.19522.44370.0022-1.136-1.26650.19690.18820.76060.1787-0.5016-0.25440.6207-0.1149-0.10460.81890.21470.751117.0019-55.331311.2332
34.3443-2.39542.28843.3113-2.42186.2882-0.0249-0.0962-0.0184-0.017-0.0304-0.10560.00130.09980.07250.4-0.1089-0.02850.55610.04350.572912.6932-42.37481.1578
43.455-0.94510.97541.6903-0.29191.92380.0223-0.60840.20240.2156-0.15530.1444-0.3289-0.30620.13130.4562-0.04770.04670.5436-0.08880.5348-1.8214-31.2871.4616
56.48573.9938-2.67295.55120.19784.0522-0.4017-0.46930.38250.44250.16460.1466-0.5299-0.4224-0.00190.57070.2021-0.01530.7421-0.03160.6611-16.3101-40.2286-14.7418
65.38771.74350.38173.7615-2.58642.40690.05960.0883-0.0913-0.2855-0.0066-0.43480.3669-0.0728-0.20730.60980.00150.04260.7203-0.1120.5496-0.5545-41.6944-21.7939
77.39713.85390.00537.4688-0.33612.7279-0.27711.1158-0.647-0.53070.3833-0.19220.37710.22740.0360.47550.0172-0.04390.6478-0.12760.488-9.1308-46.341-25.234
86.96330.46130.70683.0136-2.77075.3324-0.28760.3425-1.0156-0.21120.50910.57631.0849-0.9804-0.22920.6264-0.0104-0.01720.7659-0.06810.7588-19.3424-51.6061-18.2103
91.93722.2727-4.49762.8062-5.28752-0.1246-0.1215-0.14-0.05120.08190.14960.1988-0.00540.02381.6040.14270.57560.8410.03531.7246-9.4819-67.1144-13.1057
104.68392.0606-1.52452.3661-2.21484.9987-0.27620.1268-0.3522-0.36350.1899-0.2970.2476-0.60450.06280.45540.0524-0.02610.6487-0.02460.5649-9.4494-44.9715-14.7737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 328 )
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 51 )
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 85 )
7X-RAY DIFFRACTION7chain 'B' and (resid 86 through 105 )
8X-RAY DIFFRACTION8chain 'B' and (resid 106 through 138 )
9X-RAY DIFFRACTION9chain 'B' and (resid 150 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 189 )

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