[English] 日本語
Yorodumi- EMDB-16822: Cryo-EM structure of the murine IL-12 complete extracellular sign... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16822 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the murine IL-12 complete extracellular signaling complex (Class 1). | |||||||||
Map data | Sharpened map of the murine IL12:IL12Rbeta1:IL12Rbeta2 complex (Class 1). | |||||||||
Sample |
| |||||||||
Keywords | Complex / Cytokine / Receptor / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information 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 / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / interleukin-12 receptor binding / natural killer cell activation / T-helper cell differentiation / interleukin-23 receptor complex / 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 / cytokine receptor activity / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of T cell differentiation / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / cytokine binding / positive regulation of interleukin-10 production / : / immunoglobulin mediated immune response / negative regulation of protein secretion / coreceptor activity / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / negative regulation of inflammatory response to antigenic stimulus / positive regulation of interleukin-12 production / negative regulation of smooth muscle cell proliferation / response to cytokine / cytokine activity / endosome lumen / growth factor activity / cellular response to type II interferon / cytokine-mediated signaling pathway / Golgi lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / defense response to virus / defense response to Gram-negative bacterium / receptor complex / cell population proliferation / response to lipopolysaccharide / cell surface receptor signaling pathway / immune response / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / protein-containing complex binding / protein kinase binding / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.6 Å | |||||||||
Authors | Felix J / Bloch Y / Savvides SN | |||||||||
Funding support | Belgium, 2 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_16822.map.gz | 38.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-16822-v30.xml emd-16822.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16822_fsc.xml | 7.3 KB | Display | FSC data file |
Images | emd_16822.png | 78.8 KB | ||
Masks | emd_16822_msk_1.map | 40.6 MB | Mask map | |
Filedesc metadata | emd-16822.cif.gz | 6.6 KB | ||
Others | emd_16822_half_map_1.map.gz emd_16822_half_map_2.map.gz | 37.7 MB 37.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16822 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16822 | HTTPS FTP |
-Validation report
Summary document | emd_16822_validation.pdf.gz | 827 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_16822_full_validation.pdf.gz | 826.6 KB | Display | |
Data in XML | emd_16822_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | emd_16822_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16822 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16822 | HTTPS FTP |
-Related structure data
Related structure data | 8c7mC 8cr5C 8cr6C 8cr8C 8odxC 8odzC 8oe0C 8oe4C 8pb1C 8ppmC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_16822.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map of the murine IL12:IL12Rbeta1:IL12Rbeta2 complex (Class 1). | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.51 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_16822_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2 of the murine IL12:IL12Rbeta1:IL12Rbeta2 complex...
File | emd_16822_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 of the murine IL12:IL12Rbeta1:IL12Rbeta2 complex (Class 1). | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1 of the murine IL12:IL12Rbeta1:IL12Rbeta2 complex...
File | emd_16822_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 of the murine IL12:IL12Rbeta1:IL12Rbeta2 complex (Class 1). | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Murine IL-12 in complex with Strep-II tagged mIL-12Rbeta1 and mIL...
Entire | Name: Murine IL-12 in complex with Strep-II tagged mIL-12Rbeta1 and mIL-12Rbeta2. |
---|---|
Components |
|
-Supramolecule #1: Murine IL-12 in complex with Strep-II tagged mIL-12Rbeta1 and mIL...
Supramolecule | Name: Murine IL-12 in complex with Strep-II tagged mIL-12Rbeta1 and mIL-12Rbeta2. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 198 KDa |
-Macromolecule #1: Murine Interleukin-12 subunit alpha (IL-12A, p35), with a C-termi...
Macromolecule | Name: Murine Interleukin-12 subunit alpha (IL-12A, p35), with a C-terminal caspase-3 cleavable His tag. type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MCQSRYLLFL ATLALLNHLS LARVIPVSGP ARCLSQSRNL LKTTDDMVKT AREKLKHYSC TAEDIDHEDI TRDQTSTLKT CLPLELHKNE SCLATRETSS TTRGSCLPPQ KTSLMMTLCL GSIYEDLKMY QTEFQAINAA LQNHNHQQII LDKGMLVAID ELMQSLNHNG ...String: MCQSRYLLFL ATLALLNHLS LARVIPVSGP ARCLSQSRNL LKTTDDMVKT AREKLKHYSC TAEDIDHEDI TRDQTSTLKT CLPLELHKNE SCLATRETSS TTRGSCLPPQ KTSLMMTLCL GSIYEDLKMY QTEFQAINAA LQNHNHQQII LDKGMLVAID ELMQSLNHNG ETLRQKPPVG EADPYRVKMK LCILLHAFST RVVTINRVMG YLSSAGTSDE VDGGSGGSGL NDIFEAQKIE WHEGRTKHHH HHH UniProtKB: Interleukin-12 subunit alpha |
-Macromolecule #2: Murine Interleukin-12 subunit beta (IL-12B, p40).
Macromolecule | Name: Murine Interleukin-12 subunit beta (IL-12B, p40). / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MCPQKLTISW FAIVLLVSPL MAMWELEKDV YVVEVDWTPD APGETVNLTC DTPEEDDITW TSDQRHGVIG SGKTLTITVK EFLDAGQYTC HKGGETLSHS HLLLHKKENG IWSTEILKNF KNKTFLKCEA PNYSGRFTCS WLVQRNMDLK FNIKSSSSSP DSRAVTCGMA ...String: MCPQKLTISW FAIVLLVSPL MAMWELEKDV YVVEVDWTPD APGETVNLTC DTPEEDDITW TSDQRHGVIG SGKTLTITVK EFLDAGQYTC HKGGETLSHS HLLLHKKENG IWSTEILKNF KNKTFLKCEA PNYSGRFTCS WLVQRNMDLK FNIKSSSSSP DSRAVTCGMA SLSAEKVTLD QRDYEKYSVS CQEDVTCPTA EETLPIELAL EARQQNKYEN YSTSFFIRDI IKPDPPKNLQ MKPLKNSQVE VSWEYPDSWS TPHSYFSLKF FVRIQRKKEK MKETEEGCNQ KGAFLVEKTS TEVQCKGGNV CVQAQDRYYN SSCSKWACVP CRVRS UniProtKB: Interleukin-12 subunit beta |
-Macromolecule #3: Murine Interleukin-12 Receptor beta 1 (domains 1 to 5) with C-ter...
Macromolecule | Name: Murine Interleukin-12 Receptor beta 1 (domains 1 to 5) with C-terminal Strep-II tag. type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QLGASGPGDG CCVEKTSFPE GASGSPLGPR NLSCYRVSKT DYECSWQYDG PEDNVSHVLW CCFVPPNHTH TGQERCRYFS SGPDRTVQFW EQDGIPVLSK VNFWVESRLG NRTMKSQKIS QYLYNWTKTT PPLGHIKVSQ SHRQLRMDWN VSEEAGAEVQ FRRRMPTTNW ...String: QLGASGPGDG CCVEKTSFPE GASGSPLGPR NLSCYRVSKT DYECSWQYDG PEDNVSHVLW CCFVPPNHTH TGQERCRYFS SGPDRTVQFW EQDGIPVLSK VNFWVESRLG NRTMKSQKIS QYLYNWTKTT PPLGHIKVSQ SHRQLRMDWN VSEEAGAEVQ FRRRMPTTNW TLGDCGPQVN SGSGVLGDIR GSMSESCLCP SENMAQEIQI RRRRRLSSGA PGGPWSDWSM PVCVPPEVLP QAKIKFLVEP LNQGGRRRLT MQGQSPQLAV PEGCRGRPGA QVKKHLVLVR MLSCRCQAQT SKTVPLGKKL NLSGATYDLN VLAKTRFGRS TIQKWHLPAQ ELTETRALNV SVGGNMTSMQ WAAQAPGTTY CLEWQPWFQH RNHTHCTLIV PEEEDPAKMV THSWSSKPTL EQEECYRITV FASKNPKNPM LWATVLSSYY FGGNASRAGT PRHVSVRNQT GDSVSVEWTA SQLSTCPGVL TQYVVRCEAE DGAWESEWLV PPTKTQVTLD GLRSRVMYKV QVRADTARLP GAWSHPQRFS FEGTWSHPQF EK UniProtKB: Interleukin-12 receptor subunit beta-1 |
-Macromolecule #4: Murine Interleukin-12 Receptor beta 2 (domains 1 to 6) with C-ter...
Macromolecule | Name: Murine Interleukin-12 Receptor beta 2 (domains 1 to 6) with C-terminal Strep-II tag. type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NIDVCKLGTV TVQPAPVIPL GSAANISCSL NPKQGCSHYP SSNELILLKF VNDVLVENLH GKKVHDHTGH SSTFQVTNLS LGMTLFVCKL NCSNSQKKPP VPVCGVEISV GVAPEPPQNI SCVQEGENGT VACSWNSGKV TYLKTNYTLQ LSGPNNLTCQ KQCFSDNRQN ...String: NIDVCKLGTV TVQPAPVIPL GSAANISCSL NPKQGCSHYP SSNELILLKF VNDVLVENLH GKKVHDHTGH SSTFQVTNLS LGMTLFVCKL NCSNSQKKPP VPVCGVEISV GVAPEPPQNI SCVQEGENGT VACSWNSGKV TYLKTNYTLQ LSGPNNLTCQ KQCFSDNRQN CNRLDLGINL SPDLAESRFI VRVTAINDLG NSSSLPHTFT FLDIVIPLPP WDIRINFLNA SGSRGTLQWE DEGQVVLNQL RYQPLNSTSW NMVNATNAKG KYDLRDLRPF TEYEFQISSK LHLSGGSWSN WSESLRTRTP EEEPVGILDI WYMKQDIDYD RQQISLFWKS LNPSEARGKI LHYQVTLQEV TKKTTLQNTT RHTSWTRVIP RTGAWTASVS AANSKGASAP THINIVDLCG TGLLAPHQVS AKSENMDNIL VTWQPPKKAD SAVREYIVEW RALQPGSITK FPPHWLRIPP DNMSALISEN IKPYICYEIR VHALSESQGG CSSIRGDSKH KAPVSGPHIT AITEKKERLF ISWTHIPFPE QRGCILHYRI YWKERDSTAQ PELCEIQYRR SQNSHPISSL QPRVTYVLWM TAVTAAGESP QGNEREFCPQ GKANGTWSHP QFEK UniProtKB: Interleukin-12 receptor subunit beta-2 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
Details: HEPES-buffered saline (HBS): 25 mM HEPES, pH 7.4, 150 mM NaCl. | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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, 4 s. blotting time.. |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 7174 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |