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- EMDB-70097: EcAvs2 bound to phage PhiV-1 terminase, symmetry-expanded C1 refi... -

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Basic information

Entry
Database: EMDB / ID: EMD-70097
TitleEcAvs2 bound to phage PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain
Map dataSharpened map of EcAvs2 bound to phage PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain
Sample
  • Complex: EcAvs2 bound to phage PhiV-1 terminase
Keywordsphage defense / pattern-recognition receptor / nlr / stand / atpase / ANTIVIRAL PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.23 Å
AuthorsWilkinson ME / Gao A
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_70097.png

Downloads & links

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Map

FileDownload / File: emd_70097.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, symmetry-expanded C1 refinement of TPR-terminase domain
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-0.0726989 - 0.20572925
Average (Standard dev.)-0.00013308076 (±0.0026276647)
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_70097_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, symmetry-expanded C1...

Fileemd_70097_half_map_1.map
AnnotationEcAvs2 bound to phage PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain, half-map 1
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, symmetry-expanded C1...

Fileemd_70097_half_map_2.map
AnnotationEcAvs2 bound to phage PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain, half-map 2
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

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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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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0)
Details: Particles from the overall C4 refinement were symmetry-expanded then focus-refined with a mask on the TPR/terminase domains
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

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