+
Open data
-
Basic information
Entry | ![]() | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Vaccinia C16 protein bound to Ku70/Ku80 | |||||||||||||||||||||
![]() | Map of C16 C-terminal domains bound to Ku70/Ku80 | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | C16 vaccinia virus protein Ku70/Ku80 DNA binding inhibition / VIRAL PROTEIN | |||||||||||||||||||||
Function / homology | ![]() 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 / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / 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 / protein localization to chromosome, telomeric region / cellular response to fatty acid / positive regulation of neurogenesis / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / positive regulation of catalytic activity / telomeric DNA binding / 2-LTR circle formation / : / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / enzyme activator activity / positive regulation of telomere maintenance via telomerase / activation of innate immune response / DNA helicase activity / telomere maintenance / neurogenesis / cyclin binding / cellular response to leukemia inhibitory factor / 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 / scaffold protein binding / double-stranded DNA binding / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / response to xenobiotic stimulus / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.46 Å | |||||||||||||||||||||
![]() | Rivera-Calzada A / Arribas-Bosacoma R / Pearl LH / Llorca O | |||||||||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 90.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 24.1 KB 24.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.8 KB | Display | ![]() |
Images | ![]() | 87.3 KB | ||
Filedesc metadata | ![]() | 7.6 KB | ||
Others | ![]() ![]() | 84.1 MB 84.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ag4MC ![]() 8ag3C ![]() 8ag5C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map of C16 C-terminal domains bound to Ku70/Ku80 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half map 1
File | emd_15415_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_15415_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Vaccinia C16 protein bound to Ku70/Ku80
Entire | Name: Vaccinia C16 protein bound to Ku70/Ku80 |
---|---|
Components |
|
-Supramolecule #1: Vaccinia C16 protein bound to Ku70/Ku80
Supramolecule | Name: Vaccinia C16 protein bound to Ku70/Ku80 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 230 KDa |
-Macromolecule #1: X-ray repair cross-complementing protein 6
Macromolecule | Name: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 74.234703 KDa |
Recombinant expression | Organism: ![]() |
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 UniProtKB: X-ray repair cross-complementing protein 6 |
-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 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 85.546484 KDa |
Recombinant expression | Organism: ![]() |
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 UniProtKB: X-ray repair cross-complementing protein 5 |
-Macromolecule #3: Protein C10
Macromolecule | Name: Protein C10 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 42.47668 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 UniProtKB: Protein C10 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.4 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.9 Component:
| ||||||||||||||||||
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 |
---|---|
Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 13216 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Initial model |
| ||||||
---|---|---|---|---|---|---|---|
Details | Initial model for chains C and D was generated using AlphaFold2 | ||||||
Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | ![]() PDB-8ag4: |