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- EMDB-27422: Avs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27422
TitleAvs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease domain
Map dataAvs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease domain
Sample
  • Complex: Avs4 bound to phage PhiV-1 portal
    • Protein or peptide: ATP-binding protein Avs4
    • Protein or peptide: Portal protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homologyPortal 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
Function and homology information
Biological speciesEscherichia coli (E. coli) / Escherichia phage PhiV-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWilkinson ME / Gao L / Strecker J / Makarova KS / Macrae RK / Koonin EV / Zhang F
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5DP1HL141201-04 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01HG009761-05 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
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
DepositionJun 23, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateAug 24, 2022-
Current statusAug 24, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27422.png

Downloads & links

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Map

FileDownload / File: emd_27422.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAvs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 360 pix.
= 372.37 Å		1.03 Å/pix.
x 360 pix.
= 372.37 Å		1.03 Å/pix.
x 360 pix.
= 372.37 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03436 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.054954402 - 0.13813162
Average (Standard dev.)0.00060915825 (±0.0032523128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 372.3703 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27422_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_27422_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_27422_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Avs4 bound to phage PhiV-1 portal

EntireName: Avs4 bound to phage PhiV-1 portal
Components
  • Complex: Avs4 bound to phage PhiV-1 portal
    • Protein or peptide: ATP-binding protein Avs4
    • Protein or peptide: Portal protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Avs4 bound to phage PhiV-1 portal

SupramoleculeName: Avs4 bound to phage PhiV-1 portal / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 980 KDa

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Macromolecule #1: ATP-binding protein Avs4

MacromoleculeName: ATP-binding protein Avs4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: NCTC11132
Molecular weightTheoretical: 186.640906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (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

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Macromolecule #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage PhiV-1 (virus)
Molecular weightTheoretical: 58.556 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 31.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 169977
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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