[English] 日本語
Yorodumi
- PDB-8uui: X-ray structure of Interleukin-23 in complex with peptide 23-446 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uui
TitleX-ray structure of Interleukin-23 in complex with peptide 23-446
Components
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
  • peptide 23-446
KeywordsCYTOKINE / IL-23
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 / 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 / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / interleukin-12-mediated signaling pathway / positive regulation of NK T cell proliferation / T-helper cell differentiation / positive regulation of memory T cell differentiation / Interleukin-12 signaling / positive regulation of natural killer cell proliferation / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / cell surface receptor signaling pathway via STAT / cytokine receptor activity / natural killer cell activation / response to UV-B / positive regulation of granulocyte macrophage colony-stimulating factor production / 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 activated T cell proliferation / positive regulation of interleukin-10 production / cell surface receptor signaling pathway via JAK-STAT / 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 defense response to virus by host / positive regulation of interleukin-12 production / positive regulation of cell adhesion / regulation of cytokine production / cytokine activity / negative regulation of smooth muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of T cell mediated cytotoxicity / cellular response to type II interferon / 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 / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / defense response to virus / inflammatory response / endoplasmic reticulum lumen / 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. / Four-helical cytokine-like, core / Immunoglobulin subtype 2 ...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. / Four-helical cytokine-like, core / 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
Similarity search - Domain/homology
Interleukin-12 subunit beta / Interleukin-23 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsJoseph, J.S. / Sridhar, V.S. / Liu, M. / Hu, Y. / Gatchalian, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Identification of an Induced Orthosteric Pocket in IL-23: A New Avenue for Non-biological Therapeutic Targeting.
Authors: Lecomte, F.C. / Joseph, J.S. / Stalewski, J. / Shen, Q. / Arnoult, E. / Sridhar, V. / Liu, M. / Hu, Y. / Gasendo, J.G. / Ben Arie, H. / Keinan, N. / Keidar, L. / Aviv, I. / Ruvinov, E. / ...Authors: Lecomte, F.C. / Joseph, J.S. / Stalewski, J. / Shen, Q. / Arnoult, E. / Sridhar, V. / Liu, M. / Hu, Y. / Gasendo, J.G. / Ben Arie, H. / Keinan, N. / Keidar, L. / Aviv, I. / Ruvinov, E. / Grandjean, J. / Dores-Silva, P.R. / Mak, A. / Santoso, B. / Kim, S. / Shende, V. / Wever, W.J. / Mirzadegan, T. / Zhu, Z. / Fuchs, B. / Pinton, P. / Szabady, R.
History
DepositionNov 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Interleukin-23 subunit alpha
A: Interleukin-12 subunit beta
D: peptide 23-446
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7064
Polymers56,9573
Non-polymers7491
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-5 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.740, 110.740, 85.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Interleukin-23 subunit alpha


Mass: 19525.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A / Plasmid: pcDNA3.4 / Cell line (production host): Expi293 GnTI / Production host: Homo sapiens (human) / References: UniProt: Q9NPF7
#2: Protein 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: 34811.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Plasmid: pcDNA3.4 / Cell line (production host): Expi293 GnTI / Production host: Homo sapiens (human) / References: UniProt: P29460
#3: Protein/peptide peptide 23-446


Mass: 2620.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#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-ROHGlycam 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
[][D-1-deoxy-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.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 19% PEG 1000, 0.1 M phosphate/citrate buffer pH 4.4, 0.2 M LiSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 31, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→47.95 Å / Num. obs: 44166 / % possible obs: 100 % / Redundancy: 15.3 % / Biso Wilson estimate: 72.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.021 / Rrim(I) all: 0.03 / Χ2: 1 / Net I/σ(I): 19.8
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2379 / CC1/2: 0.477 / Χ2: 0.91 / % possible all: 100

-
Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIXdev_4788phasing
PHENIXdev_4788refinement
Coot0.9.8model building
XDSdata reduction
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→46.48 Å / SU ML: 0.4755 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.7548
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2778 3925 8.89 %
Rwork0.2203 40241 -
obs0.2254 44166 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.63 Å2
Refinement stepCycle: LAST / Resolution: 2.43→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 50 13 3406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673482
X-RAY DIFFRACTIONf_angle_d0.80614752
X-RAY DIFFRACTIONf_chiral_restr0.0498548
X-RAY DIFFRACTIONf_plane_restr0.0065601
X-RAY DIFFRACTIONf_dihedral_angle_d5.9748492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.460.41561380.43281484X-RAY DIFFRACTION99.82
2.46-2.490.44381360.38811398X-RAY DIFFRACTION99.74
2.49-2.520.40121540.38661451X-RAY DIFFRACTION100
2.52-2.560.44321400.35691398X-RAY DIFFRACTION99.94
2.56-2.590.41231380.35171455X-RAY DIFFRACTION99.87
2.59-2.630.35041440.32051466X-RAY DIFFRACTION99.63
2.63-2.670.36051330.3021389X-RAY DIFFRACTION99.87
2.67-2.720.39181440.31791438X-RAY DIFFRACTION100
2.72-2.770.29451370.27511486X-RAY DIFFRACTION99.88
2.77-2.820.32461340.2751408X-RAY DIFFRACTION99.81
2.82-2.870.35341460.28271430X-RAY DIFFRACTION99.94
2.87-2.930.42091460.29061454X-RAY DIFFRACTION100
2.93-2.990.3491440.28091443X-RAY DIFFRACTION99.94
2.99-3.060.36811420.28851406X-RAY DIFFRACTION99.94
3.06-3.140.34581480.30721444X-RAY DIFFRACTION100
3.14-3.220.42071380.28081417X-RAY DIFFRACTION100
3.22-3.320.25251360.24231436X-RAY DIFFRACTION100
3.32-3.420.27281380.22081454X-RAY DIFFRACTION100
3.42-3.550.28341380.22851456X-RAY DIFFRACTION100
3.55-3.690.25571420.2251441X-RAY DIFFRACTION99.94
3.69-3.860.26911340.21241428X-RAY DIFFRACTION100
3.86-4.060.26141400.20421434X-RAY DIFFRACTION100
4.06-4.310.23751420.19541416X-RAY DIFFRACTION100
4.31-4.650.26951350.17231474X-RAY DIFFRACTION100
4.65-5.110.22911340.17671425X-RAY DIFFRACTION100
5.11-5.850.23461520.191443X-RAY DIFFRACTION100
5.85-7.360.28221340.20471435X-RAY DIFFRACTION99.87
7.37-46.480.22831380.18551432X-RAY DIFFRACTION99.68

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more