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- EMDB-27421: Avs3 bound to phage PhiV-1 terminase, C2 refinement of Cap4 nucle... -

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Basic information

Entry
Database: EMDB / ID: EMD-27421
TitleAvs3 bound to phage PhiV-1 terminase, C2 refinement of Cap4 nuclease domain
Map dataAvs3 bound to gp19 terminase, C2 refinement of Cap4 nuclease domain
Sample
  • Complex: Avs3 bound to phage PhiV-1 terminase
    • Protein or peptide: SeAvs3
    • Protein or peptide: Terminase, large subunit
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsphage defense / pattern-recognition receptor / nlr / stand / atpase / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / 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
Terminase, large subunit gp19 / : / Terminase Bacteriophage T7, Ribonuclease H-like domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesSalmonella enterica (bacteria) / Escherichia phage PhiV-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27421.png

Downloads & links

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Map

FileDownload / File: emd_27421.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAvs3 bound to gp19 terminase, C2 refinement of Cap4 nuclease domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.092 Å		0.87 Å/pix.
x 360 pix.
= 313.092 Å		0.87 Å/pix.
x 360 pix.
= 313.092 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8697 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.021841109 - 0.042749994
Average (Standard dev.)0.000091488306 (±0.001740127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.092 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27421_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_27421_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_27421_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Avs3 bound to phage PhiV-1 terminase

EntireName: Avs3 bound to phage PhiV-1 terminase
Components
  • Complex: Avs3 bound to phage PhiV-1 terminase
    • Protein or peptide: SeAvs3
    • Protein or peptide: Terminase, large subunit
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Avs3 bound to phage PhiV-1 terminase

SupramoleculeName: Avs3 bound to phage PhiV-1 terminase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 1.21 MDa

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Macromolecule #1: SeAvs3

MacromoleculeName: SeAvs3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 236.796469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Terminase, large subunit

MacromoleculeName: 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
Source (natural)Organism: Escherichia phage PhiV-1 (virus)
Molecular weightTheoretical: 66.345469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / 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: 8 / 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

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
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: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 44479
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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