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- PDB-5mj3: INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 1 -

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Basic information

Entry
Database: PDB / ID: 5mj3
TitleINTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 1
Components
  • ALPHABODY MA12
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
KeywordsIMMUNE SYSTEM / DESIGNED ANTIPARALLEL TRIPLE-HELIX COILED-COIL / ALPHABODY / IMMUNOGLOBULIN DOMAIN / 4-HELICAL BUNDLE CYTOKINE / ANTAGONIST / N-LINKED GLYCOSYLATION / ALKYLATION
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 / positive regulation of natural killer cell activation / 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 ...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 / positive regulation of natural killer cell activation / 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 lymphocyte proliferation / positive regulation of tissue remodeling / 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 / T-helper cell differentiation / natural killer cell activation / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / negative regulation of interleukin-17 production / positive regulation of NK T cell proliferation / positive regulation of osteoclast differentiation / 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 / defense response to protozoan / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / positive regulation of interleukin-10 production / negative regulation of protein secretion / positive regulation of T-helper 17 cell lineage commitment / T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / positive regulation of T cell proliferation / regulation of cytokine production / positive regulation of interleukin-12 production / positive regulation of cell adhesion / cytokine activity / negative regulation of inflammatory response to antigenic stimulus / negative regulation of smooth muscle cell proliferation / cellular response to type II interferon / cytokine-mediated signaling pathway / positive regulation of inflammatory response / positive regulation of T cell mediated cytotoxicity / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to virus / defense response to Gram-negative bacterium / 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
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 / Growth Hormone; Chain: A; / Four-helical cytokine-like, core / 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 / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / 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: 1.74 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. / Hendrikx, P. / Lasters, I. / Savvides, S.N.
Funding support Belgium, Ecuador, 4items
OrganizationGrant numberCountry
Belgium
Belgium
Belgium
Ecuador
CitationJournal: Nat Commun / Year: 2014
Title: Structural Basis Of Il-23 Antagonism By An Alphabody Protein Scaffold.
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.N.
History
DepositionNov 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
SupersessionFeb 1, 2017ID: 4OE8
Revision 1.1Feb 1, 2017Group: Other
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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
A: Interleukin-12 subunit beta
B: Interleukin-23 subunit alpha
C: ALPHABODY MA12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9499
Polymers66,4983
Non-polymers1,4516
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-18 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.960, 56.740, 100.070
Angle α, β, γ (deg.)90.00, 99.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules BC

#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: 11945.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: in-silico design / Source: (gene. exp.) synthetic construct (others) / Plasmid: PET16B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS

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Antibody / Sugars , 2 types, 2 molecules A

#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
#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

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Non-polymers , 4 types, 422 molecules

#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 20.75% PEG 3350, 200MM SODIUM SULPHATE

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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: 1.74→41 Å / Num. obs: 63104 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rrim(I) all: 0.054 / Net I/σ(I): 13.7
Reflection shellResolution: 1.74→1.85 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Rrim(I) all: 0.636 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DUH

3duh


Resolution: 1.74→40.61 Å / Cross valid method: FREE R-VALUE
Details: Follow-up work showed an incorrectly modelled helix starting at residue Gly60 of chain B in the model deposited as 4OE8.
RfactorNum. reflection% reflection
Rfree0.198 --
Rwork0.165 --
obs-63099 97.9 %
Refinement stepCycle: LAST / Resolution: 1.74→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 96 417 4700
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)
10.08260.30660.13222.2202-1.64852.64380.0262-0.16260.03150.0957-0.2084-0.18890.10.2736-0.02860.2885-0.0002-0.02530.54320.07490.2839.7539-3.301741.3986
21.2398-0.27760.5740.2835-0.41121.4467-0.0156-0.2823-0.0601-0.0072-0.0305-0.067-0.03450.133700.2376-0.0103-0.00160.32110.02470.275831.290210.36222.8862
30.8981-0.37730.00231.1985-0.67381.10980.0791-0.07080.22520.0084-0.0774-0.0929-0.2364-0.0480.01850.3055-0.00150.02840.1412-0.01860.284519.400730.57945.1552
41.01530.1023-0.06630.74640.36840.77980.1263-0.0503-0.0573-0.11010.00970.0860.1963-0.1733-00.29610.0395-0.00860.250.00110.30296.426113.10569.9134
50.00950.00220.00890.0328-0.02540.02350.1677-0.06870.07220.62960.29650.1259-0.117-0.03530.0011.3202-0.3701-0.15281.41820.39911.024611.0457-3.649818.5862
60.2915-0.20480.21170.1405-0.04930.36140.08530.2909-0.348-0.2896-0.1503-0.19840.16260.0827-0.00340.4653-0.0070.02440.2764-0.0760.358415.25721.6172-1.4154
70.1597-0.0340.13950.08620.01410.12240.00960.2308-0.6462-0.2414-0.07570.22420.2693-0.30870.01470.3346-0.0537-0.02090.3185-0.0550.38413.8411.20662.9066
80.0639-0.0128-0.05160.0406-0.03660.0457-0.14340.0024-0.04810.13160.25470.12330.1256-0.5150.00010.2682-0.0627-0.0140.43270.02990.3582-9.08318.323518.0141
90.14210.1333-0.07950.1454-0.05790.0447-0.04030.3123-0.2675-0.3045-0.17630.6088-0.3123-0.42370.00140.3234-0.0155-0.08090.4514-0.01560.4213-3.54549.91113.6608
100.06960.135-0.13370.1324-0.23140.37230.03220.2036-0.7598-0.48760.03340.60260.1614-0.08030.13090.7805-0.0337-0.01560.7057-0.01460.5973-4.7177-0.59098.116
110.5614-0.29430.30970.3608-0.04180.19270.00420.0412-0.0541-0.15740.05180.11820.1384-0.352900.2767-0.0244-0.01410.2223-0.00940.26296.52859.30539.7656
120.3896-0.0037-0.40950.00710.04830.4571-0.0546-0.45430.14330.01960.2435-0.0442-0.0371-0.19190.00010.34620.01560.00690.4255-0.0490.33696.263713.672332.2337
131.0650.39030.18320.83580.52090.29430.1328-0.40460.03190.11890.0962-0.1958-0.0215-0.10620.00020.4772-0.00650.05950.4963-0.05410.3593.255320.002339.5761
140.27140.34290.05330.80810.44450.29750.0614-0.02450.1881-0.0379-0.17050.0548-0.0206-0.0699-00.2659-0.00530.01170.4429-0.00720.269-4.081614.295233.335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 127 ) or chain 'A' and (resid 401:405)
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 227 )
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 328 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 60 )
5X-RAY DIFFRACTION5chain 'B' and (resid 61 through 67 )
6X-RAY DIFFRACTION6chain 'B' and (resid 68 through 86 )
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 104 )
8X-RAY DIFFRACTION8chain 'B' and (resid 105 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 135 )
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 154 )
11X-RAY DIFFRACTION11chain 'B' and (resid 155 through 189 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 26 )
13X-RAY DIFFRACTION13chain 'C' and (resid 27 through 91 )
14X-RAY DIFFRACTION14chain 'C' and (resid 92 through 118 )

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