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- EMDB-25229: In situ subtomogram average of the Goslar major phage nucleus she... -

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Basic information

Entry
Database: EMDB / ID: EMD-25229
TitleIn situ subtomogram average of the Goslar major phage nucleus shell protein, chimallin (consensus class)
Map data
Sample
  • Complex: Goslar chimallin in the context of the phage nucleus
Biological speciesGoslarvirus
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsLaughlin TG / Deep A / Prichard AM / Gu Y / Enustun E / Suslov S / Khanna K / Birkholz EA / Amaro RE / Pogliano J ...Laughlin TG / Deep A / Prichard AM / Gu Y / Enustun E / Suslov S / Khanna K / Birkholz EA / Amaro RE / Pogliano J / Corbett KD / Villa E
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM129245 United States
National Science Foundation (NSF, United States)NSF DBI 1920374 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2022
Title: Architecture and self-assembly of the jumbo bacteriophage nuclear shell.
Authors: Thomas G Laughlin / Amar Deep / Amy M Prichard / Christian Seitz / Yajie Gu / Eray Enustun / Sergey Suslov / Kanika Khanna / Erica A Birkholz / Emily Armbruster / J Andrew McCammon / Rommie ...Authors: Thomas G Laughlin / Amar Deep / Amy M Prichard / Christian Seitz / Yajie Gu / Eray Enustun / Sergey Suslov / Kanika Khanna / Erica A Birkholz / Emily Armbruster / J Andrew McCammon / Rommie E Amaro / Joe Pogliano / Kevin D Corbett / Elizabeth Villa /
Abstract: Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of large bacteriophages uses a ...Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
History
DepositionOct 28, 2021-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateAug 24, 2022-
Current statusAug 24, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25229.png

Downloads & links

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Map

FileDownload / File: emd_25229.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.5 Å/pix.
x 64 pix.
= 480. Å		7.5 Å/pix.
x 64 pix.
= 480. Å		7.5 Å/pix.
x 64 pix.
= 480. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.53
Minimum - Maximum-0.29212204 - 1.0426848
Average (Standard dev.)0.013221828 (±0.19230482)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25229_msk_1.map
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AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_25229_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25229_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Goslar chimallin in the context of the phage nucleus

EntireName: Goslar chimallin in the context of the phage nucleus
Components
  • Complex: Goslar chimallin in the context of the phage nucleus

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Supramolecule #1: Goslar chimallin in the context of the phage nucleus

SupramoleculeName: Goslar chimallin in the context of the phage nucleus / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Goslarvirus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: 20 mA, PELCO EasiGLO
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 40 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER
Details: manual backside blotted using a custom built plunging device.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Number grids imaged: 1 / Average electron dose: 2.6 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
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: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number subtomograms used: 4501
ExtractionNumber tomograms: 6 / Number images used: 42416 / Method: ab initio / Software - Name: Dynamo (ver. 1.1.514)
Details: Initial reference generated from coarse alignment of pointed sampled orthogonal to the compartment surface.
CTF correctionSoftware - Name: Warp (ver. 1.09)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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