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- EMDB-16821: 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 2). | |||||||||
![]() | Main map: Anisotropy sharpened map of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex (Class 2), 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 / negative regulation of vascular endothelial growth factor signaling pathway ...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 / negative regulation of vascular endothelial growth factor signaling pathway / 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 / cellular response to hydroperoxide / positive regulation of smooth muscle cell apoptotic process / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / positive regulation of T-helper 1 type immune response / interleukin-12 receptor binding / T-helper cell differentiation / interleukin-23 receptor complex / Caspase activation via Dependence Receptors in the absence of ligand / interleukin-12-mediated signaling pathway / defense response to tumor cell / positive regulation of NK T cell proliferation / positive regulation of osteoclast differentiation / regulation of NMDA receptor activity / negative regulation of interleukin-17 production / 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 / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / syntaxin-1 binding / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / positive regulation of T cell differentiation / 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 / CaMK IV-mediated phosphorylation of CREB / PKA activation / 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 ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / negative regulation of interleukin-10 production / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / defense response to protozoan / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of interleukin-17 production / RHO GTPases activate PAKs / positive regulation of natural killer cell proliferation / positive regulation of activated T cell proliferation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of interleukin-10 production / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / extrinsic apoptotic signaling pathway via death domain receptors / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / detection of calcium ion / negative regulation of protein secretion / regulation of cardiac muscle contraction / cell surface receptor signaling pathway via JAK-STAT / RHO GTPases activate IQGAPs / T cell proliferation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / coreceptor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 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: Bloch Y / Felix J / Merceron R / Provost M / Symakani RA / De Backer R / Lambert E / Mehdipour AR / Savvides SN | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 37.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.3 KB 25.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.3 KB | Display | ![]() |
Images | ![]() | 88 KB | ||
Masks | ![]() | 40.6 MB | ![]() | |
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() ![]() | 36.5 MB 37.7 MB 37.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 818.6 KB | Display | ![]() |
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Full document | ![]() | 818.2 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oe0MC ![]() 8c7mC ![]() 8cr5C ![]() 8cr6C ![]() 8cr8C ![]() 8odxC ![]() 8odzC ![]() 8oe4C ![]() 8pb1C ![]() 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: Anisotropy sharpened map of the murine IL12:IL12Rbeta1-DAPK1:IL12Rbeta2-Calmodulin complex (Class 2), used for model refinement in Phenix. Additional map: DeepEMhancer sharpened map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.51 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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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 #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-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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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
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-8oe0: |