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- EMDB-17580: Cryo-EM structure of a pre-dimerized murine IL-12 complete extrac... -
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Open data
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Basic information
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Title | Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 1), obtained after local refinement. | |||||||||
![]() | Main map: Sharpened map of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex (Class 1, local refinement) used for model refinement in Phenix. Additional map: deepEMhancer sharpened map. | |||||||||
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![]() | Complex / Cytokine / Receptor / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() interleukin-12 beta subunit binding / Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / Interleukin-35 Signalling / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / T-helper 1 cell activation / natural killer cell activation involved in immune response ...interleukin-12 beta subunit binding / Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / Interleukin-35 Signalling / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / T-helper 1 cell activation / natural killer cell activation involved in immune response / 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 / cellular response to hydroperoxide / positive regulation of T-helper 1 type immune response / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / positive regulation of smooth muscle cell apoptotic process / interleukin-12 receptor binding / natural killer cell activation / T-helper cell differentiation / interleukin-23 receptor complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / response to UV-B / regulation of NMDA receptor activity / CaM pathway / Cam-PDE 1 activation / cytokine receptor activity / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / Sodium/Calcium exchangers / syntaxin-1 binding / Calmodulin induced events / Reduction of cytosolic Ca++ levels / calcium/calmodulin-dependent protein kinase activity / positive regulation of T cell differentiation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / negative regulation of interleukin-10 production / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of activated T cell proliferation / defense response to protozoan / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-17 production / RHO GTPases activate PAKs / cytokine binding / : / Ion transport by P-type ATPases / Long-term potentiation / positive regulation of interleukin-10 production / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / extrinsic apoptotic signaling pathway via death domain receptors / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / immunoglobulin mediated immune response / negative regulation of protein secretion / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / coreceptor activity / eNOS activation / positive regulation of autophagy / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Felix J / Bloch Y / Savvides SN | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 166 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.1 KB 26.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.6 KB | Display | ![]() |
Images | ![]() | 68.5 KB | ||
Masks | ![]() ![]() | 325 MB 325 MB | ![]() | |
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() ![]() | 268.8 MB 301.3 MB 301.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pb1MC ![]() 8c7mC ![]() 8cr5C ![]() 8cr6C ![]() 8cr8C ![]() 8odxC ![]() 8odzC ![]() 8oe0C ![]() 8oe4C ![]() 8ppmC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Main map: Sharpened map of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex (Class 1, local refinement) used for model refinement in Phenix. Additional map: deepEMhancer sharpened map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.755 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Mask #2
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Density Histograms |
-Additional map: DeepEMhancer sharpened map of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex...
File | emd_17580_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer sharpened map of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex (Class 1, local refinement) used for model building in Coot and visualization. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex...
File | emd_17580_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex (Class 1), obtained after local refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex...
File | emd_17580_half_map_2.map | ||||||||||||
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Annotation | Half map 2 of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex (Class 1), obtained after local refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Murine IL-12 in complex with mIL-12Rbeta1-DAPK1 and mIL-12Rbeta2-...
Entire | Name: Murine IL-12 in complex with mIL-12Rbeta1-DAPK1 and mIL-12Rbeta2-Calmodulin. |
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Components |
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-Supramolecule #1: Murine IL-12 in complex with mIL-12Rbeta1-DAPK1 and mIL-12Rbeta2-...
Supramolecule | Name: Murine IL-12 in complex with mIL-12Rbeta1-DAPK1 and mIL-12Rbeta2-Calmodulin. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 216 KDa |
-Macromolecule #1: Interleukin-12 subunit alpha
Macromolecule | Name: Interleukin-12 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.927496 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: RVIPVSGPAR CLSQSRNLLK TTDDMVKTAR EKLKHYSCTA EDIDHEDITR DQTSTLKTCL PLELHKNESC LATRETSSTT RGSCLPPQK TSLMMTLCLG SIYEDLKMYQ TEFQAINAAL QNHNHQQIIL DKGMLVAIDE LMQSLNHNGE TLRQKPPVGE A DPYRVKMK ...String: RVIPVSGPAR CLSQSRNLLK TTDDMVKTAR EKLKHYSCTA EDIDHEDITR DQTSTLKTCL PLELHKNESC LATRETSSTT RGSCLPPQK TSLMMTLCLG SIYEDLKMYQ TEFQAINAAL QNHNHQQIIL DKGMLVAIDE LMQSLNHNGE TLRQKPPVGE A DPYRVKMK LCILLHAFST RVVTINRVMG YLSSAGTSDE VDGGSGGSGL NDIFEAQKIE WHEGRTKHHH HHH UniProtKB: Interleukin-12 subunit alpha |
-Macromolecule #2: Interleukin-12 subunit beta
Macromolecule | Name: Interleukin-12 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.83732 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MWELEKDVYV VEVDWTPDAP GETVNLTCDT PEEDDITWTS DQRHGVIGSG KTLTITVKEF LDAGQYTCHK GGETLSHSHL LLHKKENGI WSTEILKNFK NKTFLKCEAP NYSGRFTCSW LVQRNMDLKF NIKSSSSSPD SRAVTCGMAS LSAEKVTLDQ R DYEKYSVS ...String: MWELEKDVYV VEVDWTPDAP GETVNLTCDT PEEDDITWTS DQRHGVIGSG KTLTITVKEF LDAGQYTCHK GGETLSHSHL LLHKKENGI WSTEILKNFK NKTFLKCEAP NYSGRFTCSW LVQRNMDLKF NIKSSSSSPD SRAVTCGMAS LSAEKVTLDQ R DYEKYSVS CQEDVTCPTA EETLPIELAL EARQQNKYEN YSTSFFIRDI IKPDPPKNLQ MKPLKNSQVE VSWEYPDSWS TP HSYFSLK FFVRIQRKKE KMKETEEGCN QKGAFLVEKT STEVQCKGGN VCVQAQDRYY NSSCSKWACV PCRVRS UniProtKB: Interleukin-12 subunit beta |
-Macromolecule #3: Interleukin-12 receptor subunit beta-1,Death-associated protein k...
Macromolecule | Name: Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 63.789156 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QLGASGPGDG CCVEKTSFPE GASGSPLGPR NLSCYRVSKT DYECSWQYDG PEDNVSHVLW CCFVPPNHTH TGQERCRYFS SGPDRTVQF WEQDGIPVLS KVNFWVESRL GNRTMKSQKI SQYLYNWTKT TPPLGHIKVS QSHRQLRMDW NVSEEAGAEV Q FRRRMPTT ...String: QLGASGPGDG CCVEKTSFPE GASGSPLGPR NLSCYRVSKT DYECSWQYDG PEDNVSHVLW CCFVPPNHTH TGQERCRYFS SGPDRTVQF WEQDGIPVLS KVNFWVESRL GNRTMKSQKI SQYLYNWTKT TPPLGHIKVS QSHRQLRMDW NVSEEAGAEV Q FRRRMPTT NWTLGDCGPQ VNSGSGVLGD IRGSMSESCL CPSENMAQEI QIRRRRRLSS GAPGGPWSDW SMPVCVPPEV LP QAKIKFL VEPLNQGGRR RLTMQGQSPQ LAVPEGCRGR PGAQVKKHLV LVRMLSCRCQ AQTSKTVPLG KKLNLSGATY DLN VLAKTR FGRSTIQKWH LPAQELTETR ALNVSVGGNM TSMQWAAQAP GTTYCLEWQP WFQHRNHTHC TLIVPEEEDP AKMV THSWS SKPTLEQEEC YRITVFASKN PKNPMLWATV LSSYYFGGNA SRAGTPRHVS VRNQTGDSVS VEWTASQLST CPGVL TQYV VRCEAEDGAW ESEWLVPPTK TQVTLDGLRS RVMYKVQVRA DTARLPGAWS HPQRFSFEGT GGSGGSGGAA RKKWKQ SVR LISLCQRLS UniProtKB: Interleukin-12 receptor subunit beta-1, Death-associated protein kinase 1 |
-Macromolecule #4: Interleukin-12 receptor subunit beta-2,Calmodulin-1
Macromolecule | Name: Interleukin-12 receptor subunit beta-2,Calmodulin-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 85.723344 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: NIDVCKLGTV TVQPAPVIPL GSAANISCSL NPKQGCSHYP SSNELILLKF VNDVLVENLH GKKVHDHTGH SSTFQVTNLS LGMTLFVCK LNCSNSQKKP PVPVCGVEIS VGVAPEPPQN ISCVQEGENG TVACSWNSGK VTYLKTNYTL QLSGPNNLTC Q KQCFSDNR ...String: NIDVCKLGTV TVQPAPVIPL GSAANISCSL NPKQGCSHYP SSNELILLKF VNDVLVENLH GKKVHDHTGH SSTFQVTNLS LGMTLFVCK LNCSNSQKKP PVPVCGVEIS VGVAPEPPQN ISCVQEGENG TVACSWNSGK VTYLKTNYTL QLSGPNNLTC Q KQCFSDNR QNCNRLDLGI NLSPDLAESR FIVRVTAIND LGNSSSLPHT FTFLDIVIPL PPWDIRINFL NASGSRGTLQ WE DEGQVVL NQLRYQPLNS TSWNMVNATN AKGKYDLRDL RPFTEYEFQI SSKLHLSGGS WSNWSESLRT RTPEEEPVGI LDI WYMKQD IDYDRQQISL FWKSLNPSEA RGKILHYQVT LQEVTKKTTL QNTTRHTSWT RVIPRTGAWT ASVSAANSKG ASAP THINI VDLCGTGLLA PHQVSAKSEN MDNILVTWQP PKKADSAVRE YIVEWRALQP GSITKFPPHW LRIPPDNMSA LISEN IKPY ICYEIRVHAL SESQGGCSSI RGDSKHKAPV SGPHITAITE KKERLFISWT HIPFPEQRGC ILHYRIYWKE RDSTAQ PEL CEIQYRRSQN SHPISSLQPR VTYVLWMTAV TAAGESPQGN EREFCPQGKA NGTGGSGGSG GLTEEQIAEF KEAFSLF DK DGDGTITTKE LGTVMRSLGQ NPTEAELQDM INEVDADGNG TIDFPEFLTM MARKMKDTDS EEEIREAFRV FDKDGNGY I SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK UniProtKB: Interleukin-12 receptor subunit beta-2, Calmodulin-1 |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 1 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Component:
Details: HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl | ||||||||||||
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA PLUNGER / Details: Leica EM GP2, 5 s. blotting time.. |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 8145 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000 |
Sample stage | Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8pb1: |