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- EMDB-27422: Avs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease ... -
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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Avs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease domain | ||||||||||||
![]() | Avs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease domain | ||||||||||||
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Function / homology | Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein![]() | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 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 | ![]() | 161.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.6 KB 18.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 55.9 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Others | ![]() ![]() | 139.5 MB 139.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dgfMC ![]() 8dgcC 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
File | ![]() | ||||||||||||||||||||
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Annotation | Avs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease domain | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.03436 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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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_27422_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_27422_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Avs4 bound to phage PhiV-1 portal
Entire | Name: Avs4 bound to phage PhiV-1 portal |
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Components |
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-Supramolecule #1: Avs4 bound to phage PhiV-1 portal
Supramolecule | Name: Avs4 bound to phage PhiV-1 portal / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 980 KDa |
-Macromolecule #1: ATP-binding protein Avs4
Macromolecule | Name: ATP-binding protein Avs4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 186.640906 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: (FME)VKPNWDNFK AKFSENPQGN FEWFCYLLFC QEFKMPAGIF RYKNQSGIET NPITKDNEII GWQSKFYDTK LSDNKA DLI EMIEKSKKAY PGLSKIIFYT NQEWGQGRKS HEPEGDKNAD NYLETVGNSN DPKIKIEVDQ KAYESGIEIV WRVASFF ES PFVIVENEKI ...String: (FME)VKPNWDNFK AKFSENPQGN FEWFCYLLFC QEFKMPAGIF RYKNQSGIET NPITKDNEII GWQSKFYDTK LSDNKA DLI EMIEKSKKAY PGLSKIIFYT NQEWGQGRKS HEPEGDKNAD NYLETVGNSN DPKIKIEVDQ KAYESGIEIV WRVASFF ES PFVIVENEKI AKHFFSLNES IFDLLEEKRK HTENVLYEIQ TNIEFKDRSI EIDRRHCIEL LHENLVQKKI VIVSGEGG V GKTAVIKKIY EAEKQYTPFY VFKASEFKKD SINELFGAHG LDDFSNAHQD ELRKVIVVDS AEKLLELTNI DPFKEFLTV LIKDKWQVVF TTRNNYLADL NYAFIDIYKI TPGNLVIKNL ERGELIELSD NNGFSLPQDV RLLELIKNPF YLSEYLRFYT GESIDYVSF KEKLWNKIIV KNKPSREQCF LATAFQRASE GQFFVSPACD TGILDELVKD GIVGYEAAGY FITHDIYEEW A LEKKISVD YIRKANNNEF FEKIGESLPV RRSFRNWISE RLLLDDQSIK PFIAEIVCGE GISNFWKDEL WVAVLLSDNS SI FFNYFKR YLLSSDQNLL KRLTFLLRLA CKDVDYDLLK QLGVSNSDLL SIKYVLTKPK GTGWQSVIQF IYENLDEIGI RNI NFILPV IQEWNQRNKV GETTRLSSLI ALKYYQWTID EDVYLSGRDN EKNILHTILH GAAMIKPEME EVLVKVLKNR WKEH GTPYF DLMTLILTDL DSYPVWASLP EYVLQLADLF WYRPLKETGE RYHSMDIEDE FGLFRSHHDY YPESPYQTPI YWLLQ SQFK KTIDFILDFT NKTTICFAHS HFAKNEIEEV DVFIEEGKFI KQYICNRLWC SYRGTQVSTY LLSSIHMALE KFFLEN FKN ADSKVLESWL LFLLRNTKSA SISAVVTSIV LAFPEKTFNV AKVLFQTKDF FRFDMNRMVL DRTHKSSLIS LRDGFGG TD YRNSLHEEDR IKACDDVHRN TYLENLALHY QIFRSENVTE KDAIERQQVL WDIFDKYYNQ LPDEAQETEA DKTWRLCL A RMDRRKMKIT TKEKDEGIEI SFNPEIDPKL KQYSEEAIKK NSEHMKYVTL KLWASYKREK DERYKNYGMY EDNPQIALQ ETKEIIKKLN EEGGEDFRLL NGNIPADVCS VLLLDYFNQL NNEEREYCKD IVLAYSKLPL KEGYNYQVQD GTTSAISALP VIYHNYPME RETIKTILLL TLFNDHSIGM AGGRYSVFPS MVIHKLWLDY FDDMQSLLFG FLILKPKYVI LSRKIIHESY R QVDYDIKK ININKVFLNN YKHCISNVID NKISIDDLGS MDKVDLHILN TAFQLIPVDT VNIEHKKLVS LIVKRFSTSL LS SVREDRV DYALRQSFLE RFAYFTLHAP VSDIPDYIKP FLDGFNGSEP ISELFKKFIL VEDRLNTYAK FWKVWDLFFD KVV TLCKDG DRYWYVDKII KSYLFAESPW KENSNGWHTF KDSNSQFFCD VSRTMGHCPS TLYSLAKSLN NIASCYLNQG ITWL SEILS VNKKLWEKKL ENDTVYYLEC LVRRYINNER ERIRRTKQLK QEVLVILDFL VEKGSVVGYM SRENIL |
-Macromolecule #2: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.556 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MASSQKREGF AENGAKAVYD ALKNDRNSYE TRAENCAKYT IPSLFPKDSD NASTDYTTPW QAVGARGLNN LASKLMLALF PMQTWMKLT ISEFEAKQLV AQPAELAKVE EGLSMVERIL MNYIESNSYR VTLFETLKQL VVAGNALLYI PEPEGAYNPM K LYRLSSYV ...String: MASSQKREGF AENGAKAVYD ALKNDRNSYE TRAENCAKYT IPSLFPKDSD NASTDYTTPW QAVGARGLNN LASKLMLALF PMQTWMKLT ISEFEAKQLV AQPAELAKVE EGLSMVERIL MNYIESNSYR VTLFETLKQL VVAGNALLYI PEPEGAYNPM K LYRLSSYV VQRDAFGTVL QIVTLDKTAY AALPEDVRNA MDSGQEHKGD EMIDVYTHIY LDEESGEYLK YEEIDGVEVD GT DASYPVD ACPYIPVRMV RIDGESYGRS YCEEYLGDLR SLENLQEAIV KMSMISAKVI GLVNPAGITQ VRRLTKAQTG DFV SGRPED ISFLQLEKAA DFSVAKAVSE QIEGRLSYAF MLNSAVQRTG ERVTAEEIRY VASELEDTLG GVYSILSQEL QLPM VRVLL KQLQATNQIP ELPKEAVEPT ISTGMEALGR GQDLDKLERC IAAWSALAPM QNDPDINIAT IKLRIANAIG IDTSG ILKT PEEKQQEMAE AAQGTALENA AASAGAGAGA LATASPENME AAAAQAGMVP N |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / 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: 4 / 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
Concentration | 1.7 mg/mL |
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Buffer | pH: 7.4 |
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: 31.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |