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- PDB-3d87: Crystal structure of Interleukin-23 -

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Basic information

Entry
Database: PDB / ID: 3d87
TitleCrystal structure of Interleukin-23
Components
  • Interleukin-12 subunit p40
  • Interleukin-23 subunit p19
KeywordsCYTOKINE / Interleukin-23 / FAB
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 NK T cell activation / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / 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 / Interleukin-12 signaling / positive regulation of osteoclast differentiation / cytokine receptor activity / cell surface receptor signaling pathway via STAT / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / response to UV-B / 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 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 / positive regulation of cell adhesion / regulation of cytokine production / 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 / protein heterodimerization activity / inflammatory response / 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. / 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 / 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 / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / alpha-D-mannopyranose / PHOSPHATE ION / Interleukin-12 subunit beta / Interleukin-23 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBeyer, B.M. / Ingram, R. / Ramanathan, L. / Reichert, P. / Le, H. / Madison, V.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody
Authors: Beyer, B.M. / Ingram, R. / Ramanathan, L. / Reichert, P. / Le, H.V. / Madison, V. / Orth, P.
History
DepositionMay 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-23 subunit p19
B: Interleukin-12 subunit p40
C: Interleukin-23 subunit p19
D: Interleukin-12 subunit p40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2959
Polymers108,8464
Non-polymers4485
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18570 Å2
ΔGint-108.7 kcal/mol
Surface area83720 Å2
MethodPISA
2
A: Interleukin-23 subunit p19
B: Interleukin-12 subunit p40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5574
Polymers54,4232
Non-polymers1342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-17.2 kcal/mol
Surface area22920 Å2
MethodPISA
3
C: Interleukin-23 subunit p19
D: Interleukin-12 subunit p40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7375
Polymers54,4232
Non-polymers3143
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-13.4 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.098, 240.587, 141.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 19669.137 Da / Num. of mol.: 2 / Fragment: subunit p19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798
Plasmid details: accordining to Invitrogen Bac-to-Bac manual
Plasmid: pFastBac Dual / Cell line (production host): Hi-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NPF7
#2: Antibody Interleukin-12 subunit p40 / 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: 34753.973 Da / Num. of mol.: 2 / Fragment: subunit p40 / Mutation: N200Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2
Plasmid details: accordining to Invitrogen Bac-to-Bac manual
Plasmid: pFastBac Dual / Cell line (production host): Hi-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29460
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.31 Å3/Da / Density % sol: 71.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.26M K2HPO4, 0.5M NaH2PO4, 100 mM Imidazole, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2006
RadiationMonochromator: cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20.39 Å / Num. all: 44577 / Num. obs: 41680 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 77.341 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.112 / Net I/σ(I): 9.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3980 / Rsym value: 0.675 / % possible all: 10

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER-TNT2.1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d85

3d85


Resolution: 2.9→20.39 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3232 837 2.06 %RANDOM
Rwork0.2675 ---
all0.2687 44577 --
obs0.2687 40688 93.5 %-
Displacement parametersBiso mean: 72.76 Å2
Baniso -1Baniso -2Baniso -3
1-3.04226287 Å20 Å20 Å2
2--15.16541581 Å20 Å2
3----18.20767868 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7081 0 23 0 7104
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01172782
X-RAY DIFFRACTIONt_angle_deg1.51698622
X-RAY DIFFRACTIONt_dihedral_angle_d28.47813660
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0091722
X-RAY DIFFRACTIONt_gen_planes0.01810425
X-RAY DIFFRACTIONt_it2.804727820
X-RAY DIFFRACTIONt_nbd0.0764295
LS refinement shellResolution: 2.9→3.17 Å / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.3426 246 2.12 %
Rwork0.2866 11342 -
all28.78 11588 -
obs--82.55 %

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