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- EMDB-62430: The Asymmetric Reconstruction of the Portal Vertex of Phage FCWL1... -

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Basic information

Entry
Database: EMDB / ID: EMD-62430
TitleThe Asymmetric Reconstruction of the Portal Vertex of Phage FCWL1 Before Multibody Refinement
Map data
Sample
  • Virus: Escherichia phage FCWL1 (virus)
KeywordsT1-like phage / capsid / icosahedrally averaged / VIRUS
Biological speciesEscherichia phage FCWL1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsCai C / Wang Y / Liu Y / Shao Q / Wang A / Fang Q
Funding support China, 2 items
OrganizationGrant numberCountry
Other governmentD2301008
National Natural Science Foundation of China (NSFC)32371285 China
CitationJournal: Structure / Year: 2025
Title: Structures of a T1-like siphophage reveal capsid stabilization mechanisms and high structural similarities with a myophage.
Authors: Can Cai / Yueting Wang / Yunshu Liu / Qianqian Shao / Aohan Wang / Lin Li / Yaqi Zheng / Tianyi Zhang / Ziwen Luo / Chongguang Yang / Qianglin Fang /
Abstract: Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1- ...Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1-like phage that belongs to the T1 phage family. We focus on the head, the head-to-tail interface, and its surrounding components. The hexameric capsomer displays unique gaps between neighboring A domains of the major capsid proteins. These gaps are partially filled by the N-loop of the decoration protein, which adopts a unique conformation. These structural features suggest that the phage might employ a novel strategy for stabilizing its head. Furthermore, despite being a siphophage, the head and head-to-tail connector of the phage show high structural similarity to those of a myophage. These findings enhance our understanding of the structure, capsid stabilization mechanism, and evolution of phages in the T1 family.
History
DepositionNov 16, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62430.png

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Map

FileDownload / File: emd_62430.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 320 pix.
= 515.52 Å		1.61 Å/pix.
x 320 pix.
= 515.52 Å		1.61 Å/pix.
x 320 pix.
= 515.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.611 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0148
Minimum - Maximum-0.040402193 - 0.07283411
Average (Standard dev.)0.0000041571557 (±0.0044041155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 515.51996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62430_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_62430_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_62430_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia phage FCWL1

EntireName: Escherichia phage FCWL1 (virus)
Components
  • Virus: Escherichia phage FCWL1 (virus)

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Supramolecule #1: Escherichia phage FCWL1

SupramoleculeName: Escherichia phage FCWL1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 3136680 / Sci species name: Escherichia phage FCWL1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 25.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 84600
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 74400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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