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- EMDB-27421: Avs3 bound to phage PhiV-1 terminase, C2 refinement of Cap4 nucle... -
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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Avs3 bound to phage PhiV-1 terminase, C2 refinement of Cap4 nuclease domain | ||||||||||||
![]() | Avs3 bound to gp19 terminase, C2 refinement of Cap4 nuclease domain | ||||||||||||
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![]() | phage defense / pattern-recognition receptor / nlr / stand / atpase / ANTIVIRAL PROTEIN | ||||||||||||
Function / homology | ![]() chromosome organization => GO:0051276 / viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
![]() | Wilkinson ME / Gao L / Strecker J / Makarova KS / Macrae RK / Koonin EV / Zhang F | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Authors: Linyi Alex Gao / Max E Wilkinson / Jonathan Strecker / Kira S Makarova / Rhiannon K Macrae / Eugene V Koonin / Feng Zhang / ![]() Abstract: Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in ...Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 166 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 92.2 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() | 139.1 MB 139.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dgcMC ![]() 8dgfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Avs3 bound to gp19 terminase, C2 refinement of Cap4 nuclease domain | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8697 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: Half map 1
File | emd_27421_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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Density Histograms |
-Half map: Half map 2
File | emd_27421_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Avs3 bound to phage PhiV-1 terminase
Entire | Name: Avs3 bound to phage PhiV-1 terminase |
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Components |
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-Supramolecule #1: Avs3 bound to phage PhiV-1 terminase
Supramolecule | Name: Avs3 bound to phage PhiV-1 terminase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 1.21 MDa |
-Macromolecule #1: SeAvs3
Macromolecule | Name: SeAvs3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 236.796469 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSDSLLVRTS RDGDQFHYLW AARRALRLLE PQSTLVALTI EGASTTEMGS QPVVEDGEEL IDIAEYYGSN ELATATTVRY MQLKHSTMH SDTPFPPSGL QKTIEGFATR YKALIQKIPV ETLRTKLEFW FVTNRPVSSS FSEAINDAAN QHVTRHPHDL A KLEKFTGL ...String: MSDSLLVRTS RDGDQFHYLW AARRALRLLE PQSTLVALTI EGASTTEMGS QPVVEDGEEL IDIAEYYGSN ELATATTVRY MQLKHSTMH SDTPFPPSGL QKTIEGFATR YKALIQKIPV ETLRTKLEFW FVTNRPVSSS FSEAINDAAN QHVTRHPHDL A KLEKFTGL QGAELSIFCQ LLHIEGQQDD LWSQRNILLR ESAGYLPDLD TEAPLKLKEL VNRKALTESA ANPSITRMDV LR ALGVDET DLFPAPCRIE RIENSVSRTQ EATLVQRVVE AFGAPVIIHA DAGVGKSIFS THIEEHLPTG SVSILYDCFG LGQ YRNASS YRHHHRTALV QMANEMASRG LCHPLIPNAG TGISQYMRAF LHRLSQSISI LRASEPLAVL CIIIDAADNA QMAA EEIGE TRSFIKDLIR EKLPDGVCLV ALCRPYRREL LDPPPEALTL SLQTFNRDET AAHLHQKFPD ASESDVDEFH RLSSC NPRV QALSLSQNLP LNDTLRLLGP NPKTVEDTIG EVLEKSIARL RDTAGISERA QIDTICSALA ILRPLIPLSV LSAISG VAG SAIKSFALDL GRPLIVSGET IQFFDEPAET WFQRRFRPSA ADLHQFITKL RPLTKDSSYA ASVLPALMLE GNQLSEL IE LAISSQALPE TSAVERRDIE LQRLQFALKA ALRTGRYQDA AKLALKAGGE CAGDNRQRVL LRDNIDLAAK FVGSNGVQ E LVSRNAFPDT GWPGSRNAYY AAILSEYPEL SGEARSRLRL TMEWLTNWSQ LPDDERSRQN VTDQDRAVML IACLNIHGA EAAARELRRW RPRKLSFDAG KIVAMQLLAH ARYDELDQLA IAAGNDISLV MGIVLEARKL HRPVAEQAIR RTWRLLKSQR VSIKDRNHA NNQTIAAITG MVEMALIQSV CTESESIQLL DRYLPKVPPY ALTSEYSKER VAYVRAYALQ ANLMGSQLAL S DLASTEVK KELMAEKRHG ESDDLRQLKQ YSGVLIPWYN LWAKVILGKT RKADLESELS DTQKESTAIK GHSYSEHSLS SN EIANVWF DILIEAGNVS KDDVENIIKW SQHKGNRVFT PTLHRFSSVC AEISGLGELS YHFAELALSL WRDEHSDAQI KAD GYIDLS RSLISLDEPE AKEYFNQAIE VTNKLGDENL SRWEAILDLA EYVAGKTQVP PEISYKLARC AELTREYVDR DKHF AWSDT VEILAELCPS SALAIISRWR DRTFGNHRSI LAWTIEHLVK KNKINALDAL PLITFENDWH KCDLLDSVLS SCTDD KDKI MAFEVVYHYT KFNVQNIQNL KKLDAISTSL GIEHTELKER ISGLQHTETV SKKSSLSSND NEQGHDQEWE SIFKDC DLS SIDGISAAYE KFRNVPEFYS KETFIKKAIS RVKTGKECSF ITAIGAIFHW GLYDFKYILE SIPDEWTSRL SIKTTLA GL IKEYCQRFCM RIRKSRVYEI FPFSLASRLS GISEKEIFGI TLEAIAESPE PANSDRLFSL PGLLVSKLES NEALDVLS Y ALDLFDEVLK DEDGDGPWNE KLSPPTHVED SLAGYIWARL GSPEAEMRWQ AAHAVLALCR MSRTCVIQGI FQHAINATT LPFCDRNLPF YTLHAQLWLM IAAARVALDD GKSLIPNIGY FYHYATTDQP HVLIRHFAAR TLLALHDSDL ISIPAQEENK LRNINQSTT LPVLDKVEDH RGEDSYTFGI DFGPYWLKPL GRCFGVSQKQ LEPEMLRIIR DVLGFKGSRN WDEDERNKRR Y YQDRDNHH SHGSYPRVDD YHFYLSYHAM FMTAGQLLAT KPLVGSDYDD VEDVFQDWLR RHDISRNDHR WLADRRDIPP KE RSSWLNS SSDNRDEWLA SISENVFNET LCPSPGLLTL WGRWSDVCSD RKESIIVHSA LVSPERSLSL LRALQTTKNV YDY KIPDAG DNLEIDHAHY QLKGWIKDIA EYCGIDEFDP WAGNVRFPIP EPASFIIDAM KLTTDKDHRV WYSPSDVEPA MISS IWGHL SGKNDEEKSH GYRLCASIHF IKSALETFNM DLILEVDVDR YSRNSRYERN NENELDNIPS STRLFLFRHD GTIHT LYGN YRNGEKTS |
-Macromolecule #2: Terminase, large subunit
Macromolecule | Name: Terminase, large subunit / type: protein_or_peptide / ID: 2 / Number of copies: 4 / 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: ![]() |
Molecular weight | Theoretical: 66.345469 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSQSQEAKNA LIIAQLKGDF VAFLFVLWKA LNLPKPTKCQ IDMARTLANG DHKKFILQAF RGIGKSFITC AFVVWVLWRD PQLKVLIVS ASKERADANS IFIKNIIDLL PFLSELKPRP GQRDSVISFD VGLAKPDHSP SVKSVGITGQ LTGSRADIII A DDVEVPGN ...String: MSQSQEAKNA LIIAQLKGDF VAFLFVLWKA LNLPKPTKCQ IDMARTLANG DHKKFILQAF RGIGKSFITC AFVVWVLWRD PQLKVLIVS ASKERADANS IFIKNIIDLL PFLSELKPRP GQRDSVISFD VGLAKPDHSP SVKSVGITGQ LTGSRADIII A DDVEVPGN SSTSSAREKL WTLVTEFAAL LKPLPTSRVI YLGTPQTEMT LYKELEDNKG YSTVIWPAQY PRNDAEALYY GD RLAPMLK AEYDEGFELL RGQPTDPVRF DMDDLREREL EYGKAGYTLQ FMLNPNLSDA EKYPLRLRDA IVCAVDPERA PLS YQWLPN RQNRNEELPN VGLKGDDIHA FHTCSSRTAE YQSKILVIDP SGRGKDETGY AVLYSLNGYI YLMEVGGFRG GYDD ATLEK LAKKAKQWKV QTVVHESNFG DGMFGKIFSP ILLKHHKCAL EEIRAKGMKE MRICDTIEPL MGAHKLVIRD EVIRE DYQT ARDLDGKHDV RYSAFYQMTR MTRERGAVAH DDRIDAIALG IEYLREGMLV DSRVGEEEMT LEFLEHHMEK QTIGGD QIH SFDVGGVDIY YEDEDGGSSF IEW UniProtKB: Terminase, large subunit |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |