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- EMDB-38846: Block 1 of PhiKZ capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-38846
TitleBlock 1 of PhiKZ capsid
Map data
Sample
  • Virus: Phikzvirus phiKZ
KeywordsphiKZ / capsid protein / viral assembly / Pseudomonas aeruginosa / VIRUS
Biological speciesPhikzvirus phiKZ
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYang Y / Shao Q / Guo M / Han L / Zhao X / Wang A / Li X / Wang B / Pan J / Chen Z ...Yang Y / Shao Q / Guo M / Han L / Zhao X / Wang A / Li X / Wang B / Pan J / Chen Z / Fokine A / Sun L / Fang Q
Funding support China, 4 items
OrganizationGrant numberCountry
Shenzhen Medical Research Fund (SMRF)D2301008 China
Shenzhen Science and Technology ProgramZDSYS20230626091203007 China
Ministry of Science and Technology (MoST, China)2021YFC2302500 China
R&D Program of Guangzhou LaboratorySRPG22-003 China
CitationJournal: Nat Commun / Year: 2024
Title: Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages.
Authors: Yashan Yang / Qianqian Shao / Mingcheng Guo / Lin Han / Xinyue Zhao / Aohan Wang / Xiangyun Li / Bo Wang / Ji-An Pan / Zhenguo Chen / Andrei Fokine / Lei Sun / Qianglin Fang /
Abstract: Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic ...Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses.
History
DepositionJan 25, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38846.png

Downloads & links

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Map

FileDownload / File: emd_38846.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 360 pix.
= 576.288 Å		1.6 Å/pix.
x 360 pix.
= 576.288 Å		1.6 Å/pix.
x 360 pix.
= 576.288 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6008 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0233
Minimum - Maximum-0.10769801 - 0.15732463
Average (Standard dev.)0.00037498222 (±0.00703357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 576.288 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38846_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_38846_half_map_1.map
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Half map: #2

Fileemd_38846_half_map_2.map
Projections & Slices
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Sample components

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Entire : Phikzvirus phiKZ

EntireName: Phikzvirus phiKZ
Components
  • Virus: Phikzvirus phiKZ

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Supramolecule #1: Phikzvirus phiKZ

SupramoleculeName: Phikzvirus phiKZ / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 169683 / Sci species name: Phikzvirus phiKZ / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)
Virus shellShell ID: 1 / Diameter: 1450.0 Å / T number (triangulation number): 27

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 180780
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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