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- EMDB-25221: In situ consensus subtomogram average of the 201phi2-1 chimallin -

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Basic information

Entry
Database: EMDB / ID: EMD-25221
TitleIn situ consensus subtomogram average of the 201phi2-1 chimallin
Map data
Sample
  • Organelle or cellular component: 201phi2-1 jumbo phage major shell protein, chimallin
Biological speciesPseudomonas phage 201phi2-1 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 24.0 Å
AuthorsLaughlin TG / Deep A / Prichard AM / Seitz C / Gu Y / Enustun E / Suslov S / Khanna K / Birkholz EA / Amaro RE ...Laughlin TG / Deep A / Prichard AM / Seitz C / 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 27, 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_25221.png

Downloads & links

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Map

FileDownload / File: emd_25221.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 7.5 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.32528675 - 0.99991417
Average (Standard dev.)0.011351637 (±0.1862408)
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_25221_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_25221_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25221_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 201phi2-1 jumbo phage major shell protein, chimallin

EntireName: 201phi2-1 jumbo phage major shell protein, chimallin
Components
  • Organelle or cellular component: 201phi2-1 jumbo phage major shell protein, chimallin

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Supramolecule #1: 201phi2-1 jumbo phage major shell protein, chimallin

SupramoleculeName: 201phi2-1 jumbo phage major shell protein, chimallin / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas phage 201phi2-1 (virus)

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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 / Instrument: HOMEMADE PLUNGER / Details: manual plunger, backside blotted for ~7 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average electron dose: 1.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 8 / Number images used: 17169 / Reference model: ab intio generated / Method: segementation / Software: (Name: Dynamo (ver. 1.1.514), Warp (ver. 1.09))
Details: constrained orientation search after defining initial subvolume orientations as normal to the segmentation surface.
CTF correctionSoftware: (Name: Warp (ver. 1.09), RELION (ver. 3.1.1))
Final 3D classificationSoftware - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number subtomograms used: 8454
FSC plot (resolution estimation)

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