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- EMDB-16824: Cryo-EM structure of a pre-dimerized human IL-23 complete extrace... -

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Entry
Database: EMDB / ID: EMD-16824
TitleCryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex.
Map dataMain map: Unfiltered, non-sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex used for model refinement in Phenix. Additional map: deepEMhancer sharpened map.
Sample
  • Complex: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
    • Protein or peptide: Interleukin-12 subunit beta
    • Protein or peptide: Interleukin-23 subunit alpha
    • Protein or peptide: Interleukin-23 receptor,Calmodulin-1
    • Protein or peptide: Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / Cytokine / Receptor / SIGNALING PROTEIN
Function / homology
Function and homology information


prolactin receptor activity / 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 ...prolactin receptor activity / 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 / cellular response to hydroperoxide / tissue remodeling / positive regulation of smooth muscle cell apoptotic process / regulation of response to tumor cell / positive regulation of NK T cell activation / positive regulation of autophagic cell death / DAPK1-calmodulin complex / positive regulation of T-helper 1 type immune response / sexual reproduction / positive regulation of mononuclear cell proliferation / interleukin-12 receptor complex / interleukin-23 receptor complex / interleukin-12 receptor binding / interleukin-23-mediated signaling pathway / 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 / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of natural killer cell proliferation / positive regulation of osteoclast differentiation / regulation of NMDA receptor activity / negative regulation of interleukin-17 production / cell surface receptor signaling pathway via STAT / calcium/calmodulin-dependent protein kinase activity / cytokine receptor activity / natural killer cell activation / response to UV-B / positive regulation of granulocyte macrophage colony-stimulating factor production / CaM pathway / positive regulation of neutrophil chemotaxis / Cam-PDE 1 activation / syntaxin-1 binding / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / T-helper 1 type immune response / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / negative regulation of interleukin-10 production / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / defense response to protozoan / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / Interleukin-10 signaling / regulation of cell communication by electrical coupling involved in cardiac conduction / cytokine binding / positive regulation of interleukin-17 production / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of activated T cell proliferation / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / peptide hormone binding / positive regulation of interleukin-10 production / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / extrinsic apoptotic signaling pathway via death domain receptors / DARPP-32 events / response to type II interferon / Smooth Muscle Contraction / cell surface receptor signaling pathway via JAK-STAT / catalytic complex
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 / Death-associated protein kinase 1 / Long hematopoietin receptor, soluble alpha chains family signature. ...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 / Death-associated protein kinase 1 / Long hematopoietin receptor, soluble alpha chains family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Four-helical cytokine-like, core / : / Death-like domain superfamily / Ankyrin repeat / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / Fibronectin type-III domain profile. / Ankyrin repeats (3 copies) / Fibronectin type III / Fibronectin type III superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin-1 / Interleukin-12 subunit beta / Interleukin-12 receptor subunit beta-1 / Death-associated protein kinase 1 / Interleukin-23 receptor / Interleukin-23 subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBloch Y / Felix J / Savvides SN
Funding support Belgium, 2 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
Research Foundation - Flanders (FWO)G0B4918N Belgium
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23.
Authors: Yehudi Bloch / Jan Felix / Romain Merceron / Mathias Provost / Royan Alipour Symakani / Robin De Backer / Elisabeth Lambert / Ahmad R Mehdipour / Savvas N Savvides /
Abstract: Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into ...Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.
History
DepositionMar 10, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16824.png

Downloads & links

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Map

FileDownload / File: emd_16824.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map: Unfiltered, non-sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex used for model refinement in Phenix. Additional map: deepEMhancer sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 320 pix.
= 314.08 Å		0.98 Å/pix.
x 320 pix.
= 314.08 Å		0.98 Å/pix.
x 320 pix.
= 314.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9815 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.21190277 - 0.52166134
Average (Standard dev.)0.00028738737 (±0.010982596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 314.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16824_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex,...

Fileemd_16824_additional_1.map
AnnotationDeepEMhancer sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex, used for model building in Coot and visualization.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex....

Fileemd_16824_half_map_1.map
AnnotationHalf map 2 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex....

Fileemd_16824_half_map_2.map
AnnotationHalf map 1 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.

EntireName: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
Components
  • Complex: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
    • Protein or peptide: Interleukin-12 subunit beta
    • Protein or peptide: Interleukin-23 subunit alpha
    • Protein or peptide: Interleukin-23 receptor,Calmodulin-1
    • Protein or peptide: Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.

SupramoleculeName: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 168 KDa

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Macromolecule #1: Interleukin-12 subunit beta

MacromoleculeName: Interleukin-12 subunit beta / type: protein_or_peptide / ID: 1
Details: N-glycosylation mutant: Asparagine 303 (N303) is mutated to Aspartic acid (D303).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.74093 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IWELKKDVYV VELDWYPDAP GEMVVLTCDT PEEDGITWTL DQSSEVLGSG KTLTIQVKEF GDAGQYTCHK GGEVLSHSLL LLHKKEDGI WSTDILKDQK EPKNKTFLRC EAKNYSGRFT CWWLTTISTD LTFSVKSSRG SSDPQGVTCG AATLSAERVR G DNKEYEYS ...String:
IWELKKDVYV VELDWYPDAP GEMVVLTCDT PEEDGITWTL DQSSEVLGSG KTLTIQVKEF GDAGQYTCHK GGEVLSHSLL LLHKKEDGI WSTDILKDQK EPKNKTFLRC EAKNYSGRFT CWWLTTISTD LTFSVKSSRG SSDPQGVTCG AATLSAERVR G DNKEYEYS VECQEDSACP AAEESLPIEV MVDAVHKLKY ENYTSSFFIR DIIKPDPPKN LQLKPLKNSR QVEVSWEYPD TW STPHSYF SLTFCVQVQG KSKREKKDRV FTDKTSATVI CRKDASISVR AQDRYYSSSW SEWASVPCS

UniProtKB: Interleukin-12 subunit beta

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Macromolecule #2: Interleukin-23 subunit alpha

MacromoleculeName: Interleukin-23 subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.650117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RAVPGGSSPA WTQCQQLSQK LCTLAWSAHP LVGHMDLREE GDEETTNDVP HIQCGDGCDP QGLRDNSQFC LQRIHQGLIF YEKLLGSDI FTGEPSLLPD SPVGQLHASL LGLSQLLQPE GHHWETQQIP SLSPSQPWQR LLLRFKILRS LQAFVAVAAR V FAHGAATL SPGDEVDGHH HHHHHHHH

UniProtKB: Interleukin-23 subunit alpha

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Macromolecule #3: Interleukin-23 receptor,Calmodulin-1

MacromoleculeName: Interleukin-23 receptor,Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.991391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GITNINCSGH IWVEPATIFK MGMNISIYCQ AAIKNCQPRK LHFYKNGIKE RFQITRINKT TARLWYKNFL EPHASMYCTA ECPKHFQET LICGKDISSG YPPDIPDEVT CVIYEYSGNM TCTWNAGKLT YIDTKYVVHV KSLETEEEQQ YLTSSYINIS T DSLQGGKK ...String:
GITNINCSGH IWVEPATIFK MGMNISIYCQ AAIKNCQPRK LHFYKNGIKE RFQITRINKT TARLWYKNFL EPHASMYCTA ECPKHFQET LICGKDISSG YPPDIPDEVT CVIYEYSGNM TCTWNAGKLT YIDTKYVVHV KSLETEEEQQ YLTSSYINIS T DSLQGGKK YLVWVQAANA LGMEESKQLQ IHLDDIVIPS AAVISRAETI NATVPKTIIY WDSQTTIEKV SCEMRYKATT NQ TWNVKEF DTNFTYVQQS EFYLEPNIKY VFQVRCQETG KRYWQPWSSL FFHKTPETVP QVTSKAFQHD TWNSGLTVAS IST GHLTSD NRGDGTGGSG GSGGLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTI DFPEF LTMMARKMKD TDSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQ MMTA K

UniProtKB: Interleukin-23 receptor, Calmodulin-1

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Macromolecule #4: Interleukin-12 receptor subunit beta-1,Death-associated protein k...

MacromoleculeName: Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.187316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CRTSECCFQD PPYPDADSGS ASGPRDLRCY RISSDRYECS WQYEGPTAGV SHFLRCCLSS GRCCYFAAGS ATRLQFSDQA GVSVLYTVT LWVESWARNQ TEKSPEVTLQ LYNSVKYEPP LGDIKVSKLA GQLRMEWETP DNQVGAEVQF RHRTPSSPWK L GDCGPQDD ...String:
CRTSECCFQD PPYPDADSGS ASGPRDLRCY RISSDRYECS WQYEGPTAGV SHFLRCCLSS GRCCYFAAGS ATRLQFSDQA GVSVLYTVT LWVESWARNQ TEKSPEVTLQ LYNSVKYEPP LGDIKVSKLA GQLRMEWETP DNQVGAEVQF RHRTPSSPWK L GDCGPQDD DTESCLCPLE MNVAQEFQLR RRQLGSQGSS WSKWSSPVCV PPENPPQPQV RFSVEQLGQD GRRRLTLKEQ PT QLELPEG CQGLAPGTEV TYRLQLHMLS CPCKAKATRT LHLGKMPYLS GAAYNVAVIS SNQFGPGLNQ TWHIPADTHT EPV ALNISV GTNGTTMYWP ARAQSMTYCI EWQPVGQDGG LATCSLTAPQ DPDPAGMATY SWSRESGAMG QEKCYYITIF ASAH PEKLT LWSTVLSTYH FGGNASAAGT PHHVSVKNHS LDSVSVDWAP SLLSTCPGVL KEYVVRCRDE DSKQVSEHPV QPTET QVTL SGLRAGVAYT VQVRADTAWL RGVWSQPQRF SIEGTGGSGG SGGAARKKWK QSVRLISLCQ RLS

UniProtKB: Interleukin-12 receptor subunit beta-1, Death-associated protein kinase 1

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMC8H18N2O4SHEPES
5.0 mMCaClcalcium chloride

Details: HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA PLUNGER / Details: Leica EM GP2, 4.5 s. blotting time..

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6660 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2053974
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 315005
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8oe4:
Cryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex.

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