+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15416 | |||||||||||||||||||||
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Title | Vaccinia C16 protein bound to Ku70/Ku80 | |||||||||||||||||||||
Map data | Map of C16 vaccinia protein bound to Ku70/Ku80 | |||||||||||||||||||||
Sample |
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Function / homology | Function and homology information Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / positive regulation of neurogenesis / protein localization to chromosome, telomeric region / cellular response to fatty acid / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / telomeric DNA binding / positive regulation of catalytic activity / 2-LTR circle formation / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / enzyme activator activity / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / DNA helicase activity / activation of innate immune response / telomere maintenance / cellular response to leukemia inhibitory factor / neurogenesis / cyclin binding / small-subunit processome / protein-DNA complex / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-strand break repair / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / chromosome, telomeric region / damaged DNA binding / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Vaccinia virus Western Reserve | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||||||||||||||
Authors | Rivera-Calzada A / Arribas-Bosacoma R / Pearl LH / Llorca O | |||||||||||||||||||||
Funding support | Spain, United Kingdom, 6 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus. Authors: Angel Rivera-Calzada / Raquel Arribas-Bosacoma / Alba Ruiz-Ramos / Paloma Escudero-Bravo / Jasminka Boskovic / Rafael Fernandez-Leiro / Antony W Oliver / Laurence H Pearl / Oscar Llorca / Abstract: Detection of cytosolic DNA is a central element of the innate immunity system against viral infection. The Ku heterodimer, a component of the NHEJ pathway of DNA repair in the nucleus, functions as ...Detection of cytosolic DNA is a central element of the innate immunity system against viral infection. The Ku heterodimer, a component of the NHEJ pathway of DNA repair in the nucleus, functions as DNA sensor that detects dsDNA of viruses that replicate in the cytoplasm. Vaccinia virus expresses two proteins, C4 and C16, that inactivate DNA sensing and enhance virulence. The structural basis for this is unknown. Here we determine the structure of the C16 - Ku complex using cryoEM. Ku binds dsDNA by a preformed ring but C16 sterically blocks this access route, abrogating binding to a dsDNA end and its insertion into DNA-PK, thereby averting signalling into the downstream innate immunity system. C4 replicates these activities using a domain with 54% identity to C16. Our results reveal how vaccinia virus subverts the capacity of Ku to recognize viral DNA. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15416.map.gz | 82 MB | EMDB map data format | |
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Header (meta data) | emd-15416-v30.xml emd-15416.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
Images | emd_15416.png | 91.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15416 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15416 | HTTPS FTP |
-Related structure data
Related structure data | 8ag5MC 8ag3C 8ag4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15416.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Map of C16 vaccinia protein bound to Ku70/Ku80 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Vaccinia C16 protein bound to Ku70/Ku80
Entire | Name: Vaccinia C16 protein bound to Ku70/Ku80 |
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Components |
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-Supramolecule #1: Vaccinia C16 protein bound to Ku70/Ku80
Supramolecule | Name: Vaccinia C16 protein bound to Ku70/Ku80 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 230 KDa |
-Macromolecule #1: Ku70-Xrcc6
Macromolecule | Name: Ku70-Xrcc6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 74.234703 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSAWSHPQFE KGSAGSAAGS GAGWSHPQFE KLEVLFQGPG GSMSGWESYY KTEGDEEAEE EQEENLEASG DYKYSGRDSL IFLVDASKA MFESQSEDEL TPFDMSIQCI QSVYISKIIS SDRDLLAVVF YGTEKDKNSV NFKNIYVLQE LDNPGAKRIL E LDQFKGQQ ...String: MSAWSHPQFE KGSAGSAAGS GAGWSHPQFE KLEVLFQGPG GSMSGWESYY KTEGDEEAEE EQEENLEASG DYKYSGRDSL IFLVDASKA MFESQSEDEL TPFDMSIQCI QSVYISKIIS SDRDLLAVVF YGTEKDKNSV NFKNIYVLQE LDNPGAKRIL E LDQFKGQQ GQKRFQDMMG HGSDYSLSEV LWVCANLFSD VQFKMSHKRI MLFTNEDNPH GNDSAKASRA RTKAGDLRDT GI FLDLMHL KKPGGFDISL FYRDIISIAE DEDLRVHFEE SSKLEDLLRK VRAKETRKRA LSRLKLKLNK DIVISVGIYN LVQ KALKPP PIKLYRETNE PVKTKTRTFN TSTGGLLLPS DTKRSQIYGS RQIILEKEET EELKRFDDPG LMLMGFKPLV LLKK HHYLR PSLFVYPEES LVIGSSTLFS ALLIKCLEKE VAALCRYTPR RNIPPYFVAL VPQEEELDDQ KIQVTPPGFQ LVFLP FADD KRKMPFTEKI MATPEQVGKM KAIVEKLRFT YRSDSFENPV LQQHFRNLEA LALDLMEPEQ AVDLTLPKVE AMNKRL GSL VDEFKELVYP PDYNPEGKVT KRKHDNEGSG SKRPKVEYSE EELKTHISKG TLGKFTVPML KEACRAYGLK SGLKKQE LL EALTKHFQD |
-Macromolecule #2: X-ray repair cross-complementing protein 5
Macromolecule | Name: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 85.546484 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAHHHHHHHH HHGALEVLFQ GPHMVRSGNK AAVVLCMDVG FTMSNSIPGI ESPFEQAKKV ITMFVQRQVF AENKDEIALV LFGTDGTDN PLSGGDQYQN ITVHRHLMLP DFDLLEDIES KIQPGSQQAD FLDALIVSMD VIQHETIGKK FEKRHIEIFT D LSSRFSKS ...String: MAHHHHHHHH HHGALEVLFQ GPHMVRSGNK AAVVLCMDVG FTMSNSIPGI ESPFEQAKKV ITMFVQRQVF AENKDEIALV LFGTDGTDN PLSGGDQYQN ITVHRHLMLP DFDLLEDIES KIQPGSQQAD FLDALIVSMD VIQHETIGKK FEKRHIEIFT D LSSRFSKS QLDIIIHSLK KCDISLQFFL PFSLGKEDGS GDRGDGPFRL GGHGPSFPLK GITEQQKEGL EIVKMVMISL EG EDGLDEI YSFSESLRKL CVFKKIERHS IHWPCRLTIG SNLSIRIAAY KSILQERVKK TWTVVDAKTL KKEDIQKETV YCL NDDDET EVLKEDIIQG FRYGSDIVPF SKVDEEQMKY KSEGKCFSVL GFCKSSQVQR RFFMGNQVLK VFAARDDEAA AVAL SSLIH ALDDLDMVAI VRYAYDKRAN PQVGVAFPHI KHNYECLVYV QLPFMEDLRQ YMFSSLKNSK KYAPTEAQLN AVDAL IDSM SLAKKDEKTD TLEDLFPTTK IPNPRFQRLF QCLLHRALHP REPLPPIQQH IWNMLNPPAE VTTKSQIPLS KIKTLF PLI EAKKKDQVTA QEIFQDNHED GPTAKKLKTE QGGAHFSVSS LAEGSVTSVG SVNPAENFRV LVKQKKASFE EASNQLI NH IEQFLDTNET PYFMKSIDCI RAFREEAIKF SEEQRFNNFL KALQEKVEIK QLNHFWEIVV QDGITLITKE EASGSSVT A EEAKKFLAPK DKPSGDTAAV FEEGGDVDDL LDMI |
-Macromolecule #3: Protein C10
Macromolecule | Name: Protein C10 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vaccinia virus Western Reserve / Strain: Western Reserve |
Molecular weight | Theoretical: 42.47668 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDIYDDKGLQ TIKLFNNEFD CIRNDIRELF KHVTDSDSIQ LPMEDNSDII ENIRKILYRR LKNVECVDID STITFMKYDP NDDNKRTCS NWVPLTNNYM EYCLVIYLET PICGGKIKLY HPTGNIKSDK DIMFAKTLDF KSKKVLTGRK TIAVLDISVS Y NRSMTTIH ...String: MDIYDDKGLQ TIKLFNNEFD CIRNDIRELF KHVTDSDSIQ LPMEDNSDII ENIRKILYRR LKNVECVDID STITFMKYDP NDDNKRTCS NWVPLTNNYM EYCLVIYLET PICGGKIKLY HPTGNIKSDK DIMFAKTLDF KSKKVLTGRK TIAVLDISVS Y NRSMTTIH YNDDVDIDIH TDKNGKELCY CYITIDDHYL VDVETIGVIV NRSGKCLLVN NHLGIGIVKD KRISDSFGDV CM DTIFDFS EARELFSLTN DDNRNIAWDT DKLDDDTDIW TPVTEDDYKF LSRLVLYAKS QSDTVFDYYV LTGDTEPPTV FIF KVTRFY FNMPKGGENL YFQGWSHPQF EKGGGSGGGS GGSSAWSHPQ FEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 13216 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 12495814 |
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Startup model | Type of model: OTHER / Details: Ab intio model generated from the data set |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Software: (Name: RELION, cryoSPARC) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 152123 |