[English] 日本語
Yorodumi
- PDB-3duh: Structure of Interleukin-23 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3duh
TitleStructure of Interleukin-23
Components
  • Interleukin-12 subunit beta
  • Interleukin-23 subunit alpha
KeywordsIMMUNE SYSTEM/CYTOKINE / four-helix bundle cytokine / Ig domain / Cytokine / Glycoprotein / Immunoglobulin domain / Secreted / Antiviral defense / Immune response / Inflammatory response / Innate immunity / Tissue remodeling / IMMUNE SYSTEM / IMMUNE SYSTEM-CYTOKINE 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 / 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 T-helper 1 type immune response / sexual reproduction / 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 / CD22 mediated BCR regulation / positive regulation of T-helper 17 type immune response / positive regulation of osteoclast differentiation / interleukin-12-mediated signaling pathway / negative regulation of interleukin-17 production / positive regulation of NK T cell proliferation / 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 / Fc epsilon receptor (FCERI) signaling / T-helper 1 type immune response / Classical antibody-mediated complement activation / negative regulation of interleukin-10 production / Initial triggering of complement / defense response to protozoan / positive regulation of activated T cell proliferation / cytokine binding / positive regulation of interleukin-17 production / Interleukin-10 signaling / immunoglobulin complex / cell surface receptor signaling pathway via JAK-STAT / positive regulation of interleukin-10 production / FCGR activation / negative regulation of protein secretion / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of defense response to virus by host / Scavenging of heme from plasma / positive regulation of T-helper 17 cell lineage commitment / positive regulation of T cell proliferation / T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / regulation of cytokine production / positive regulation of interleukin-12 production / antigen binding / positive regulation of cell adhesion / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / cytokine activity / negative regulation of inflammatory response to antigenic stimulus / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / negative regulation of smooth muscle cell proliferation / cellular response to type II interferon / cytokine-mediated signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / blood microparticle / adaptive immune response / Potential therapeutics for SARS / receptor complex / inflammatory response / immune 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
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 ...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 / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin kappa variable 1-39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLupardus, P.J. / Garcia, K.C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The structure of interleukin-23 reveals the molecular basis of p40 subunit sharing with interleukin-12.
Authors: Lupardus, P.J. / Garcia, K.C.
History
DepositionJul 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,3416
Polymers110,8994
Non-polymers4422
Water3,603200
1
A: Interleukin-12 subunit beta
C: Interleukin-23 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6703
Polymers55,4492
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-5 kcal/mol
Surface area23760 Å2
MethodPISA
2
B: Interleukin-12 subunit beta
D: Interleukin-23 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6703
Polymers55,4492
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-6 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.089, 59.974, 160.365
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody Interleukin-12 subunit beta / IL-12B / IL-12 subunit p40 / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / NK ...IL-12B / IL-12 subunit p40 / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / NK cell stimulatory factor chain 2 / NKSF2


Mass: 35811.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Plasmid: pACSG2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HiFive / References: UniProt: P29460
#2: Protein Interleukin-23 subunit alpha / IL-23 subunit alpha / Interleukin-23 subunit p19 / IL-23p19


Mass: 19638.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Plasmid: pACSG2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HiFive / References: UniProt: Q9NPF7
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2M potassium nitrate, 0.1M Hepes-NaOH pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 4, 2008
RadiationMonochromator: Si(111), Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 49424 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.5 / Num. unique all: 7208 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human p40 from PDB ID 1F45

1f45


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.997 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26833 2502 5.1 %RANDOM
Rwork0.22794 ---
obs0.23007 46921 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.587 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å22.55 Å2
2---0.13 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 28 200 7010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226977
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9489500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60324.342304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.813151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2121532
X-RAY DIFFRACTIONr_chiral_restr0.0930.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025266
X-RAY DIFFRACTIONr_nbd_refined0.2030.22732
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.2130
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.220
X-RAY DIFFRACTIONr_mcbond_it0.9351.54416
X-RAY DIFFRACTIONr_mcangle_it1.60926958
X-RAY DIFFRACTIONr_scbond_it1.70832962
X-RAY DIFFRACTIONr_scangle_it2.6414.52542
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 189 -
Rwork0.282 3425 -
obs--100 %

+
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