+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21645 | |||||||||
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Title | IL-12 receptor complex | |||||||||
Map data | IL-12 receptor complex. | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Glassman CR / Mathiharan YK / Panova O / Skiniotis G / Garcia KC | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2021 Title: Structural basis for IL-12 and IL-23 receptor sharing reveals a gateway for shaping actions on T versus NK cells. Authors: Caleb R Glassman / Yamuna Kalyani Mathiharan / Kevin M Jude / Leon Su / Ouliana Panova / Patrick J Lupardus / Jamie B Spangler / Lauren K Ely / Christoph Thomas / Georgios Skiniotis / K Christopher Garcia / Abstract: Interleukin-12 (IL-12) and IL-23 are heterodimeric cytokines that are produced by antigen-presenting cells to regulate the activation and differentiation of lymphocytes, and they share IL-12Rβ1 as a ...Interleukin-12 (IL-12) and IL-23 are heterodimeric cytokines that are produced by antigen-presenting cells to regulate the activation and differentiation of lymphocytes, and they share IL-12Rβ1 as a receptor signaling subunit. We present a crystal structure of the quaternary IL-23 (IL-23p19/p40)/IL-23R/IL-12Rβ1 complex, together with cryoelectron microscopy (cryo-EM) maps of the complete IL-12 (IL-12p35/p40)/IL-12Rβ2/IL-12Rβ1 and IL-23 receptor (IL-23R) complexes, which reveal "non-canonical" topologies where IL-12Rβ1 directly engages the common p40 subunit. We targeted the shared IL-12Rβ1/p40 interface to design a panel of IL-12 partial agonists that preserved interferon gamma (IFNγ) induction by CD8 T cells but impaired cytokine production from natural killer (NK) cells in vitro. These cell-biased properties were recapitulated in vivo, where IL-12 partial agonists elicited anti-tumor immunity to MC-38 murine adenocarcinoma absent the NK-cell-mediated toxicity seen with wild-type IL-12. Thus, the structural mechanism of receptor sharing used by IL-12 family cytokines provides a protein interface blueprint for tuning this cytokine axis for therapeutics. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21645.map.gz | 22.2 MB | EMDB map data format | |
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Header (meta data) | emd-21645-v30.xml emd-21645.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21645_fsc.xml | 6.8 KB | Display | FSC data file |
Images | emd_21645.png | 29.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21645 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21645 | HTTPS FTP |
-Validation report
Summary document | emd_21645_validation.pdf.gz | 334 KB | Display | EMDB validaton report |
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Full document | emd_21645_full_validation.pdf.gz | 333.6 KB | Display | |
Data in XML | emd_21645_validation.xml.gz | 9.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21645 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21645 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21645.map.gz / Format: CCP4 / Size: 24.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | IL-12 receptor complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : IL-12 receptor extracellular domain complex
Entire | Name: IL-12 receptor extracellular domain complex |
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Components |
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-Supramolecule #1: IL-12 receptor extracellular domain complex
Supramolecule | Name: IL-12 receptor extracellular domain complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: IL-12 (IL-12p35,p40), IL-12Rb1 (with affinity enhancing Y109S and Q132L mutations), IL-12Rb2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 153 kDa/nm |
-Macromolecule #1: Interleukin-12 receptor subunit beta-2
Macromolecule | Name: Interleukin-12 receptor subunit beta-2 / type: protein_or_peptide / ID: 1 / Details: IL-12Rb2 (24-317), 6xHis / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: KIDACKRGDV TVKPSHVILL GSTVNITCSL KPRQGCFHYS RRNKLILYKF DRRINFHHGH SLNSQVTGLP LGTTLFVCKL ACINSDEIQI CGAEIFVGVA PEQPQNLSCI QKGEQGTVAC TWERGRDTHL YTEYTLQLSG PKNLTWQKQC KDIYCDYLDF GINLTPESPE ...String: KIDACKRGDV TVKPSHVILL GSTVNITCSL KPRQGCFHYS RRNKLILYKF DRRINFHHGH SLNSQVTGLP LGTTLFVCKL ACINSDEIQI CGAEIFVGVA PEQPQNLSCI QKGEQGTVAC TWERGRDTHL YTEYTLQLSG PKNLTWQKQC KDIYCDYLDF GINLTPESPE SNFTAKVTAV NSLGSSSSLP STFTFLDIVR PLPPWDIRIK FQKASVSRCT LYWRDEGLVL LNRLRYRPSN SRLWNMVNVT KAKGRHDLLD LKPFTEYEFQ ISSKLHLYKG SWSDWSESLR AQTPHHHHHH |
-Macromolecule #2: Interleukin-12 subunit alpha
Macromolecule | Name: Interleukin-12 subunit alpha / type: protein_or_peptide / ID: 2 / Details: IL-12a (22-212) / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: RNLPVATPDP GMFPCLHHSQ NLLRAVSNML QKARQTLEFY PCTSEEIDHE DITKDKTSTV EACLPLELTK NESCLNSRET SFITNGSCLA SRKTSFMMAL CLSSIYEDLK MYQVEFKTMN AKLLMDPKRQ IFLDQNMLAV IDELMQALNF NSETVPQKSS LEEPDFYKTK ...String: RNLPVATPDP GMFPCLHHSQ NLLRAVSNML QKARQTLEFY PCTSEEIDHE DITKDKTSTV EACLPLELTK NESCLNSRET SFITNGSCLA SRKTSFMMAL CLSSIYEDLK MYQVEFKTMN AKLLMDPKRQ IFLDQNMLAV IDELMQALNF NSETVPQKSS LEEPDFYKTK IKLCILLHAF RIRAVTIDRV MSYLNAS |
-Macromolecule #3: Interleukin-12 subunit beta
Macromolecule | Name: Interleukin-12 subunit beta / type: protein_or_peptide / ID: 3 / Details: IL-12b (23-328), Biotin Acceptor Peptide, 6xHis / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: IWELKKDVYV VELDWYPDAP GEMVVLTCDT PEEDGITWTL DQSSEVLGSG KTLTIQVKEF GDAGQYTCHK GGEVLSHSLL LLHKKEDGIW STDILKDQKE PKNKTFLRCE AKNYSGRFTC WWLTTISTDL TFSVKSSRGS SDPQGVTCGA ATLSAERVRG DNKEYEYSVE ...String: IWELKKDVYV VELDWYPDAP GEMVVLTCDT PEEDGITWTL DQSSEVLGSG KTLTIQVKEF GDAGQYTCHK GGEVLSHSLL LLHKKEDGIW STDILKDQKE PKNKTFLRCE AKNYSGRFTC WWLTTISTDL TFSVKSSRGS SDPQGVTCGA ATLSAERVRG DNKEYEYSVE CQEDSACPAA EESLPIEVMV DAVHKLKYEN YTSSFFIRDI IKPDPPKNLQ LKPLKNSRQV EVSWEYPDTW STPHSYFSLT FCVQVQGKSK REKKDRVFTD KTSATVICRK NASISVRAQD RYYSSSWSEW ASVPCSGRLH HILDAQKMVW NHRHHHHHH |
-Macromolecule #4: Interleukin-12 receptor subunit beta-1
Macromolecule | Name: Interleukin-12 receptor subunit beta-1 / type: protein_or_peptide / ID: 4 / Details: IL-12Rb1 Y109S Q132L (25-542), 6xHis / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: RTSECCFQDP PYPDADSGSA SGPRDLRCYR ISSDRYECSW QYEGPTAGVS HFLRCCLSSG RCCYFAAGSA TRLQFSDQAG VSVLSTVTLW VESWARNQTE KSPEVTLLLY NSVKYEPPLG DIKVSKLAGQ LRMEWETPDN QVGAEVQFRH RTPSSPWKLG DCGPQDDDTE ...String: RTSECCFQDP PYPDADSGSA SGPRDLRCYR ISSDRYECSW QYEGPTAGVS HFLRCCLSSG RCCYFAAGSA TRLQFSDQAG VSVLSTVTLW VESWARNQTE KSPEVTLLLY NSVKYEPPLG DIKVSKLAGQ LRMEWETPDN QVGAEVQFRH RTPSSPWKLG DCGPQDDDTE SCLCPLEMNV AQEFQLRRRQ LGSQGSSWSK WSSPVCVPPE NPPQPQVRFS VEQLGQDGRR RLTLKEQPTQ LELPEGCQGL APGTEVTYRL QLHMLSCPCK AKATRTLHLG KMPYLSGAAY NVAVISSNQF GPGLNQTWHI PADTHTEPVA LNISVGTNGT TMYWPARAQS MTYCIEWQPV GQDGGLATCS LTAPQDPDPA GMATYSWSRE SGAMGQEKCY YITIFASAHP EKLTLWSTVL STYHFGGNAS AAGTPHHVSV KNHSLDSVSV DWAPSLLSTC PGVLKEYVVR CRDEDSKQVS EHPVQPTETQ VTLSGLRAGV AYTVQVRADT AWLRGVWSQP QRFSIEVQAA AHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |