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- EMDB-48875: 70S Ribosome of Goslar infected chmA KD E. coli -

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Basic information

Entry
Database: EMDB / ID: EMD-48875
Title70S Ribosome of Goslar infected chmA KD E. coli
Map data
Sample
  • Complex: 70S Ribosome of Goslar infected chmA KD E.coli
Keywordstranslation / bacteria / phage / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 20.56 Å
AuthorsHutchings J / Rodriguez ZK / Klusch N / Villa E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Host Microbe / Year: 2025
Title: Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection.
Authors: Emily G Armbruster / Phoolwanti Rani / Jina Lee / Niklas Klusch / Joshua Hutchings / Lizbeth Y Hoffman / Hannah Buschkaemper / Eray Enustun / Benjamin A Adler / Koe Inlow / Arica R VanderWal ...Authors: Emily G Armbruster / Phoolwanti Rani / Jina Lee / Niklas Klusch / Joshua Hutchings / Lizbeth Y Hoffman / Hannah Buschkaemper / Eray Enustun / Benjamin A Adler / Koe Inlow / Arica R VanderWal / Madelynn Y Hoffman / Daksh Daksh / Ann Aindow / Amar Deep / Zaida K Rodriguez / Chase J Morgan / Majid Ghassemian / Thomas G Laughlin / Emeric Charles / Brady F Cress / David F Savage / Jennifer A Doudna / Kit Pogliano / Kevin D Corbett / Elizabeth Villa / Joe Pogliano /
Abstract: Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses. Bacteriophages of the Chimalliviridae family ...Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses. Bacteriophages of the Chimalliviridae family sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of the viral protein ChmA. We show that inhibiting phage nucleus formation arrests infections at an early stage in which the injected phage genome is enclosed within a membrane-bound early phage infection (EPI) vesicle. Early phage genes are expressed from the EPI vesicle, demonstrating its functionality as a prokaryotic, transcriptionally active, membrane-bound organelle. We also show that the phage nucleus is essential, with genome replication beginning after the injected DNA is transferred from the EPI vesicle to the phage nucleus. Our results show that Chimalliviridae require two sophisticated subcellular compartments of distinct compositions and functions that facilitate successive stages of the viral life cycle.
History
DepositionFeb 2, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48875.png

Downloads & links

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Map

FileDownload / File: emd_48875.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
10 Å/pix.
x 48 pix.
= 480. Å		10 Å/pix.
x 48 pix.
= 480. Å		10 Å/pix.
x 48 pix.
= 480. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 10 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.67
Minimum - Maximum-0.54066765 - 3.0577493
Average (Standard dev.)0.08874826 (±0.43046272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions484848
Spacing484848
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48875_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_48875_half_map_2.map
Projections & Slices
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Sample components

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Entire : 70S Ribosome of Goslar infected chmA KD E.coli

EntireName: 70S Ribosome of Goslar infected chmA KD E.coli
Components
  • Complex: 70S Ribosome of Goslar infected chmA KD E.coli

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Supramolecule #1: 70S Ribosome of Goslar infected chmA KD E.coli

SupramoleculeName: 70S Ribosome of Goslar infected chmA KD E.coli / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE-PROPANE
DetailsIn situ structure

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 7050
ExtractionNumber tomograms: 8 / Number images used: 7050 / Software: (Name: crYOLO (ver. 1.9.1), Warp (ver. 1.1.0))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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