+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22402 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human DPP9-CARD8 complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information CARD8 inflammasome complex assembly / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / dipeptidyl-peptidase IV / negative regulation of lipopolysaccharide-mediated signaling pathway ...CARD8 inflammasome complex assembly / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / dipeptidyl-peptidase IV / negative regulation of lipopolysaccharide-mediated signaling pathway / self proteolysis / dipeptidyl-peptidase activity / Regulation of the apoptosome activity / negative regulation of programmed cell death / Hydrolases; Acting on peptide bonds (peptidases) / regulation of canonical NF-kappaB signal transduction / negative regulation of interleukin-1 beta production / pattern recognition receptor activity / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / cell leading edge / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / antiviral innate immune response / negative regulation of tumor necrosis factor-mediated signaling pathway / aminopeptidase activity / negative regulation of canonical NF-kappaB signal transduction / serine-type peptidase activity / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / peptidase activity / regulation of apoptotic process / microtubule / defense response to virus / protein homodimerization activity / protein-containing complex / proteolysis / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Sharif H / Hollingsworth LR | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Immunity / Year: 2021 Title: Dipeptidyl peptidase 9 sets a threshold for CARD8 inflammasome formation by sequestering its active C-terminal fragment. Authors: Humayun Sharif / L Robert Hollingsworth / Andrew R Griswold / Jeffrey C Hsiao / Qinghui Wang / Daniel A Bachovchin / Hao Wu / Abstract: CARD8 detects intracellular danger signals and forms a caspase-1 activating inflammasome. Like the related inflammasome sensor NLRP1, CARD8 autoprocesses into noncovalently associated N-terminal (NT) ...CARD8 detects intracellular danger signals and forms a caspase-1 activating inflammasome. Like the related inflammasome sensor NLRP1, CARD8 autoprocesses into noncovalently associated N-terminal (NT) and C-terminal (CT) fragments and binds the cellular dipeptidyl peptidases DPP8 and 9 (DPP8/9). Certain danger-associated signals, including the DPP8/9 inhibitor Val-boroPro (VbP) and HIV protease, induce proteasome-mediated NT degradation and thereby liberate the inflammasome-forming CT. Here, we report cryoelectron microscopy (cryo-EM) structures of CARD8 bound to DPP9, revealing a repressive ternary complex consisting of DPP9, full-length CARD8, and CARD8-CT. Unlike NLRP1-CT, CARD8-CT does not interact with the DPP8/9 active site and is not directly displaced by VbP. However, larger DPP8/9 active-site probes can directly weaken this complex in vitro, and VbP itself nevertheless appears to disrupt this complex, perhaps indirectly, in cells. Thus, DPP8/9 inhibitors can activate the CARD8 inflammasome by promoting CARD8 NT degradation and by weakening ternary complex stability. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22402.map.gz | 15.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22402-v30.xml emd-22402.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22402_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_22402.png | 167.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22402 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22402 | HTTPS FTP |
-Validation report
Summary document | emd_22402_validation.pdf.gz | 354.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22402_full_validation.pdf.gz | 354.1 KB | Display | |
Data in XML | emd_22402_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_22402_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22402 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22402 | HTTPS FTP |
-Related structure data
Related structure data | 7jn7MC 7jkqC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10596 (Title: Human DPP9-CARD8 complex-VbP / Data size: 2.1 TB Data #1: Unaligned multi frame micographs of CARD8-DPP9-VbP-noTILT [micrographs - multiframe] Data #2: Unaligned multi frame micographs of CARD8-DPP9-VbP-TILT [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22402.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8187 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : DPP9-CARD8 complex
Entire | Name: DPP9-CARD8 complex |
---|---|
Components |
|
-Supramolecule #1: DPP9-CARD8 complex
Supramolecule | Name: DPP9-CARD8 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 / Recombinant plasmid: pcDNA3.1 |
-Macromolecule #1: Dipeptidyl peptidase 9
Macromolecule | Name: Dipeptidyl peptidase 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: dipeptidyl-peptidase IV |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 101.761984 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMGSMA TTGTPTADRG DAAATDDPAA RFQVQKHSWD GLRSIIHGSR KYSGLIVNKA PHDFQFVQK TDESGPHSHR LYYLGMPYGS RENSLLYSEI PKKVRKEALL LLSWKQMLDH FQATPHHGVY SREEELLRER K RLGVFGIT ...String: MSYYHHHHHH DYDIPTTENL YFQGAMGSMA TTGTPTADRG DAAATDDPAA RFQVQKHSWD GLRSIIHGSR KYSGLIVNKA PHDFQFVQK TDESGPHSHR LYYLGMPYGS RENSLLYSEI PKKVRKEALL LLSWKQMLDH FQATPHHGVY SREEELLRER K RLGVFGIT SYDFHSESGL FLFQASNSLF HCRDGGKNGF MVSPMKPLEI KTQCSGPRMD PKICPADPAF FSFINNSDLW VA NIETGEE RRLTFCHQGL SNVLDDPKSA GVATFVIQEE FDRFTGYWWC PTASWEGSEG LKTLRILYEE VDESEVEVIH VPS PALEER KTDSYRYPRT GSKNPKIALK LAEFQTDSQG KIVSTQEKEL VQPFSSLFPK VEYIARAGWT RDGKYAWAMF LDRP QQWLQ LVLLPPALFI PSTENEEQRL ASARAVPRNV QPYVVYEEVT NVWINVHDIF YPFPQSEGED ELCFLRANEC KTGFC HLYK VTAVLKSQGY DWSEPFSPGE DEFKCPIKEE IALTSGEWEV LARHGSKIWV NEETKLVYFQ GTKDTPLEHH LYVVSY EAA GEIVRLTTPG FSHSCSMSQN FDMFVSHYSS VSTPPCVHVY KLSGPDDDPL HKQPRFWASM MEAASCPPDY VPPEIFH FH TRSDVRLYGM IYKPHALQPG KKHPTVLFVY GGPQVQLVNN SFKGIKYLRL NTLASLGYAV VVIDGRGSCQ RGLRFEGA L KNQMGQVEIE DQVEGLQFVA EKYGFIDLSR VAIHGWSYGG FLSLMGLIHK PQVFKVAIAG APVTVWMAYD TGYTERYMD VPENNQHGYE AGSVALHVEK LPNEPNRLLI LHGFLDENVH FFHTNFLVSQ LIRAGKPYQL QIYPNERHSI RCPESGEHYE VTLLHFLQE YL |
-Macromolecule #2: Caspase recruitment domain-containing protein 8
Macromolecule | Name: Caspase recruitment domain-containing protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60.716875 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEKKECPEKS SSSEEELPRR DSGSSRNIDA SKLIRLQGSR KLLVDNSIRE LQYTKTGIFF QAEACVTNDT VYRELPCVSE TLCDISHFF QEDDETEAEP LLFRAVPECQ LSGGDIPSVS EEQESSEGQD SGDICSEENQ IVSSYASKVC FEIEEDYKNR Q FLGPEGNV ...String: MEKKECPEKS SSSEEELPRR DSGSSRNIDA SKLIRLQGSR KLLVDNSIRE LQYTKTGIFF QAEACVTNDT VYRELPCVSE TLCDISHFF QEDDETEAEP LLFRAVPECQ LSGGDIPSVS EEQESSEGQD SGDICSEENQ IVSSYASKVC FEIEEDYKNR Q FLGPEGNV DVELIDKSTN RYSVWFPTAG WYLWSATGLG FLVRDEVTVT IAFGSWSQHL ALDLQHHEQW LVGGPLFDVT AE PEEAVAE IHLPHFISLQ AGEVDVSWFL VAHFKNEGMV LEHPARVEPF YAVLESPSFS LMGILLRIAS GTRLSIPITS NTL IYYHPH PEDIKFHLYL VPSDALLTKA IDDEEDRFHG VRLQTSPPME PLNFGSSYIV SNSANLKVMP KELKLSYRSP GEIQ HFSKF YAGQMKEPIQ LEITEKRHGT LVWDTEVKPV DLQLVAASAP PPFSGAAFVK ENHRQLQARM GDLKGVLDDL QDNEV LTEN EKELVEQEKT RQSKNEALLS MVEKKGDLAL DVLFRSISER DPYLVSYLRQ QNL |
-Macromolecule #3: [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]bo...
Macromolecule | Name: [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid type: ligand / ID: 3 / Number of copies: 2 / Formula: GK2 |
---|---|
Molecular weight | Theoretical: 214.07 Da |
Chemical component information | ChemComp-GK2: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 25 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM TCEP |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 4 / #0 - Number real images: 3306 / #0 - Average exposure time: 2.22 sec. / #0 - Average electron dose: 58.5 e/Å2 / #0 - Details: stage tilt 0 degrees / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 4 / #1 - Number real images: 2488 / #1 - Average exposure time: 2.25 sec. / #1 - Average electron dose: 64.99 e/Å2 / #1 - Details: stage tilt 37 degrees |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Calibrated magnification: 10500 / Illumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: -0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |