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- PDB-5mj4: INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 2 -

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Basic information

Entry
Database: PDB / ID: 5mj4
TitleINTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 2
Components
  • ALPHABODY MA12
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
KeywordsIMMUNE SYSTEM / SINGLE-CHAIN ANTIPARALLEL TRIPLE-HELIX COILED-COIL / IMMUNOGLOBULIN-LIKE / 4-ALPHA HELICAL BUNDLE / ANTAGONIST / N-LINKED GLYCOSYLATION / CYTOKINE-ANTAGONIST 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
Helicase, Ruva Protein; domain 3 - #1170 / 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 ...Helicase, Ruva Protein; domain 3 - #1170 / 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; / Helicase, Ruva Protein; domain 3 / 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 / Orthogonal Bundle / 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: 3.4 Å
AuthorsDesmet, J. / Verstraete, K. / Bloch, Y. / Lorent, E. / Wen, Y. / Devreese, B. / Vandenbroucke, K. / Loverix, S. / Hettmann, T. / Deroo, S. ...Desmet, J. / Verstraete, K. / Bloch, Y. / Lorent, E. / Wen, Y. / Devreese, B. / Vandenbroucke, K. / Loverix, S. / Hettmann, T. / Deroo, S. / Somers, K. / Henderikx, P. / Lasters, I. / Savvides, S.
CitationJournal: Nature Communications / Year: 2014
Title: STRUCTURAL BASIS OF IL-23 ANTAGONISM BY AN ALPHABODY PROTEIN
Authors: Desmet, J. / Verstraete, K. / Bloch, Y. / Lorent, E. / Wen, Y. / Devreese, B. / Vandenbroucke, K. / Loverix, S. / Hettmann, T. / Deroo, S. / Somers, K. / Henderikx, P. / Lasters, I. / Savvides, S.
History
DepositionNov 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
SupersessionFeb 1, 2017ID: 4OG9
Revision 1.1Feb 1, 2017Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_symm_contact / 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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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
Revision 2.2Oct 23, 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
C: ALPHABODY MA12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3524
Polymers66,4413
Non-polymers9111
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-18 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.850, 57.850, 366.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P29460
#2: Protein Interleukin-23 subunit alpha / IL-23-A / Interleukin-23 subunit p19 / IL-23p19


Mass: 19812.342 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: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9NPF7
#3: Protein ALPHABODY MA12


Mass: 11888.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PET16B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2M POTASSIUM FORMATE, 20.75% W/V PEG 3350, PH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3.4→57 Å / Num. obs: 9551 / % possible obs: 99.85 % / Redundancy: 22.29 % / Rrim(I) all: 0.116 / Net I/σ(I): 20.7
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 23.4 % / Mean I/σ(I) obs: 5.2 / Rrim(I) all: 0.921 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OE8

4oe8
PDB Unreleased entry


Resolution: 3.4→57 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6
RfactorNum. reflection% reflection
Rfree0.2959 943 9.98 %
Rwork0.2547 --
obs0.2584 9451 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 61 0 4115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044216
X-RAY DIFFRACTIONf_angle_d0.855757
X-RAY DIFFRACTIONf_dihedral_angle_d10.8992524
X-RAY DIFFRACTIONf_chiral_restr0.051676
X-RAY DIFFRACTIONf_plane_restr0.004720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3907-3.56940.36841340.31881149X-RAY DIFFRACTION100
3.5694-3.7930.3131420.29441167X-RAY DIFFRACTION100
3.793-4.08580.30511490.26571171X-RAY DIFFRACTION100
4.0858-4.49680.271240.25641201X-RAY DIFFRACTION100
4.4968-5.14710.28581230.22871220X-RAY DIFFRACTION100
5.1471-6.48340.27681330.26511249X-RAY DIFFRACTION100
6.4834-57.15050.3011380.23921351X-RAY DIFFRACTION99
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)
18.76180.77251.6726.44483.63379.49540.2231-0.7632-0.8740.32170.544-0.28530.11780.2781-0.72692.26020.3475-0.43351.71130.01321.119316.136-31.245414.0071
23.7206-1.11120.90414.8419-0.36445.59540.2086-1.15540.0271-0.07540.14720.5841-0.0764-2.0477-0.37992.14830.13280.0661.4540.26710.95643.2462-31.41881.1588
35.1125-3.74921.65283.53161.74562.4626-1.2487-1.12050.32073.63011.1838-1.2184-0.6613-4.0870.08071.5472-0.0451-0.09351.45560.05570.2351-5.3446-18.9521-8.5919
47.0247-1.24170.01694.2838-2.44069.0305-0.7236-0.67310.94571.29030.59-1.1271-0.27-0.51380.02581.38790.1904-0.31081.2385-0.18731.00542.1406-19.5732-8.7368
59.8159-4.22493.7883.6641-5.01856.061-1.1848-1.021-0.4982.17510.71121.041-0.3054-1.1845-1.2440.5506-0.0613-0.10451.3520.00041.1329-18.1007-8.8098-25.1173
65.8583-2.9474-0.64916.82341.49377.77430.14040.44880.3780.2065-0.3870.52920.1346-2.28950.11360.51830.02140.01581.41980.20810.9611-19.7627-10.8285-27.9151
71.41443.9938-6.25157.5551-1.15666.5154-0.77960.96880.31870.66460.5717-0.66120.2107-0.48530.68750.8637-0.0035-0.11091.54030.22021.0841-1.7724-22.3154-35.5416
88.142-0.0936-3.34279.19610.38655.7447-0.63770.88780.54080.48840.7639-1.41590.55621.22830.07260.75050.1627-0.05171.88670.5641.05525.8592-19.8416-40.1044
92.32394.8498-3.23655.8182.96361.7292-0.64082.2050.3262-0.18471.4109-0.50490.2065-1.335-0.02740.93620.0994-0.02641.89010.3081.06794.741-19.1326-48.8499
105.32341.15080.63914.031-0.91142.37890.83180.8730.4862-0.8636-0.93-0.33170.3495-0.18260.05790.76780.0209-0.00390.96050.32260.67861.9617-25.2915-36.2013
119.77231.53720.73849.14172.44435.03720.6741.2154-0.48621.4172-0.4907-0.00350.1850.4982-0.3341.299-0.2398-0.02590.92260.09140.7789-5.8157-40.7039-25.5488
123.2513-0.7058-0.71132.178-0.16085.82630.24220.8825-1.686-0.45620.08990.88252.06350.1183-0.51021.6962-0.32260.04281.25570.02911.7157-7.5075-48.3884-27.3059
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 151 )
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 227 )
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 255 )
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 328 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 145 )
10X-RAY DIFFRACTION10chain 'B' and (resid 146 through 188 )
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 47 )
12X-RAY DIFFRACTION12chain 'C' and (resid 48 through 118 )

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