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- EMDB-70096: EcAvs2 bound to phage PhiV-1 terminase, overall C4 reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-70096
TitleEcAvs2 bound to phage PhiV-1 terminase, overall C4 reconstruction
Map dataSharpened map of EcAvs2 bound to phage PhiV-1 terminase, overall C4 reconstruction
Sample
  • Complex: EcAvs2 bound to phage PhiV-1 terminase
    • Protein or peptide: AVAST type 2 anti-phage system protein Avs2
    • Protein or peptide: Terminase, large subunit
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
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 speciesEscherichia coli (E. coli) / Escherichia phage PhiV-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsWilkinson ME / Gao A / Strecker J / Makarova KS / Macrae RK / Koonin EV / Zhang F
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structural basis of phage terminase recognition by the bacterial immune receptor Avs2
Authors: Chiu C / Evans SA / Wilkinson ME / Li D / Zhang F / Gao A
History
DepositionApr 8, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70096.png

Downloads & links

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Map

FileDownload / File: emd_70096.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of EcAvs2 bound to phage PhiV-1 terminase, overall C4 reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 400 pix.
= 397.8 Å		0.99 Å/pix.
x 400 pix.
= 397.8 Å		0.99 Å/pix.
x 400 pix.
= 397.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9945 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.07600234 - 0.21048361
Average (Standard dev.)-0.00009862735 (±0.0035868548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 397.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70096_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EcAvs2 bound to phage PhiV-1 terminase, overall C4...

Fileemd_70096_half_map_1.map
AnnotationEcAvs2 bound to phage PhiV-1 terminase, overall C4 reconstruction, half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EcAvs2 bound to phage PhiV-1 terminase, overall C4...

Fileemd_70096_half_map_2.map
AnnotationEcAvs2 bound to phage PhiV-1 terminase, overall C4 reconstruction, half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EcAvs2 bound to phage PhiV-1 terminase

EntireName: EcAvs2 bound to phage PhiV-1 terminase
Components
  • Complex: EcAvs2 bound to phage PhiV-1 terminase
    • Protein or peptide: AVAST type 2 anti-phage system protein Avs2
    • Protein or peptide: Terminase, large subunit
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: EcAvs2 bound to phage PhiV-1 terminase

SupramoleculeName: EcAvs2 bound to phage PhiV-1 terminase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 960 KDa

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Macromolecule #1: AVAST type 2 anti-phage system protein Avs2

MacromoleculeName: AVAST type 2 anti-phage system protein Avs2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 173.314906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEPISITVAT YVATKLIDQF ISQEGYGCIK KALFPQKRYV DRLYQLIEET AIEFEETYPV ESGAIPFYHS EPLFEMLNEH IFFKEFPDK EILLDKFKEY PSITPPTQQQ LSLFYEMLSL KINNCSKLKK LHIEETYKEK IFDINEELIQ VKLILRSIDE K LTFHLSDD ...String:
MEPISITVAT YVATKLIDQF ISQEGYGCIK KALFPQKRYV DRLYQLIEET AIEFEETYPV ESGAIPFYHS EPLFEMLNEH IFFKEFPDK EILLDKFKEY PSITPPTQQQ LSLFYEMLSL KINNCSKLKK LHIEETYKEK IFDINEELIQ VKLILRSIDE K LTFHLSDD WLNEKNSQAI ADLGGRYTPE LNVKLEIAEI FDGLGRTNDF SKIFYSHIDS FLVAGKKLHS CDVISSELFE IN QSLKEIS DIYQEINFSK LDEIPINKFN NYVSSCQTAI GGAVSILWEL REKSEQVGET KHYSDKYSST LRMLREFDYA CNE LRIFIN STTVKLANNP FLLLEGKAGI GKSHLLADVI KNRIASGYPS LLILGQQLTS DESPWSQIFK RLQLKITSRE FLEK LNLYG KKTGKRVLVF IDAINEGNGN KFWNDNINSF VDEIRCFEWL GLIMSVRTTY RNVTISHENV VRNNFEIHEH IGFQN VELE AVSLFYDYYN IERPSSPNLN PEFKNPLFLK LLCEGIKKNG LTKVPVGFNG ISNIFNFLVE GVNKSLASPK KYAFDP SFP LVKDALNEII KFKLEIGRNS ISLKDAHSVV QSVVNDYVAD KTFLSALIDE GLLTKGIVRN DDNSTEEVVY VAFERFD DH LTVNFLLNDV ENIESEFKPD GRLKKYFHDE CDFYIKSGIV EALSIQLPER YEKELYEFLP EFSNNLKLLE AFIDSLIW R DIKAIDFEKI RPFINEHVFK FKDSFDHFLE AVISISGLVG HPFNANFLHD WLKDYSLANR DSFWTTELKY KYSEDSAFR HLIDWAWART DKSFVSDESI ELVATSLCWF LTSSNRELRD CSTKALVSLL EPRIPVLRKI IDKFYGVNDP YVWERIFAVA LGCTLRTDN IKELKYLAET VYQKVFCSKY VYPNILLRDY AREIIEFANH LGLELESIEL SKTRPPYNSI WPDKIPSKEE L ESLYDKEP YRELWSSIME DGDFSRYTIG TNYNHSDWSG CKFNETPVDR KQVFKTFKCK LTDQQKDLYD ATDPFIYDDK CE GIKFGRV VGRKAQEEIK ASKKLFKNSL SYDLLSEFEN EIEPYLDHNN NLLETDKHFD LRLAQQFIFN RVIELGWDPE KHG NFDQQI GTGRGRREAF QERIGKKYQW IAYYEYMARL ADNFTRFEGY GDERKENPYQ GPWEPYVRDI DPTILLKETG TKKI SNKEM WWLNDEVFDW TCSNEDWVKS STTITNSYAF IEVKDDNGDE WIVLESHPSW KEPKIIGNDD WGHPRKEVWY QIRSY IVKV EEFENFRCWA IAQDFMGRWM PECTDRYQLF NREYYWSEAF KSFKSDYYGG SDWTSVTDRE SGAKIADVSV TSINYL WEE EFDKSKIETL NFLKPSNLIF EKMGLKSGEV EGSFNDENGT MVCFAAEAVY ASKPHLLVKK EPFLTMLRDN GFEIVWT LL GEKGVIGGSL ISSHHYGRQE FSGAFYYEDS QLTGSHKTSF TR

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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: 12 / 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: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 956 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
200.0 mMsodium chlorideNaCl
0.1 mMATP
2.0 mMmagnesium chlorideMgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16853 / Average exposure time: 0.52 sec. / Average electron dose: 32.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2840455
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 353169
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 354000 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9o4e:
EcAvs2 bound to phage PhiV-1 terminase

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