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- EMDB-35431: 201Phi2-1 gp105 cube-like assembly (O, 24mer) -

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Basic information

Entry
Database: EMDB / ID: EMD-35431
Title201Phi2-1 gp105 cube-like assembly (O, 24mer)
Map dataThe cryo-EM map of the phage-encoded nucleus-like shell protein gp105 octahedral assembly reconstructed with O symmetry imposed (O map).
Sample
  • Complex: 201phi2-1 gp105
Biological speciesPseudomonas phage 201phi2-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.76 Å
AuthorsLiu Z / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300204 China
CitationJournal: Front Microbiol / Year: 2023
Title: Structural studies of the nucleus-like assembly of jumbo bacteriophage 201φ2-1.
Authors: Zhe Liu / Ye Xiang /
Abstract: The jumbo phages encode proteins that assemble to form a nucleus-like compartment in infected cells. Here we report the cryo-EM structure and biochemistry characterization of gp105, a protein that is ...The jumbo phages encode proteins that assemble to form a nucleus-like compartment in infected cells. Here we report the cryo-EM structure and biochemistry characterization of gp105, a protein that is encoded by the jumbo phage 201φ2-1 and is involved in the formation of the nucleus-like compartment in phage 201φ2-1 infected . We found that, although most gp105 molecules are in the monomeric state in solution, a small portion of gp105 assemble to form large sheet-like assemblies and small cube-like particles. Reconstruction of the cube-like particles showed that the particle consists of six flat head-to-tail tetramers arranged into an octahedral cube. The four molecules at the contact interface of two head-to-tail tetramers are 2-fold symmetry-related and constitute a concave tetramer. Further reconstructions without applying symmetry showed that molecules in the particles around the distal ends of a 3-fold axis are highly dynamic and have the tendency to open up the assembly. Local classifications and refinements of the concave tetramers in the cube-like particle resulted in a map of the concave tetramer at a resolution of 4.09 Å. Structural analysis of the concave tetramer indicates that the N and C terminal fragments of gp105 are important for mediating the intermolecular interactions, which was further confirmed by mutagenesis studies. Biochemistry assays showed that, in solution, the cube-like particles of gp105 are liable to either disassemble to form the monomers or recruit more molecules to form the high molecular weight lattice-like assembly. We also found that monomeric gp105s can self-assemble to form large sheet-like assemblies , and the assembly of gp105 is a reversible dynamic process and temperature-dependent. Taken together, our results revealed the dynamic assembly of gp105, which helps to understand the development and function of the nucleus-like compartment assembled by phage-encoded proteins.
History
DepositionFeb 20, 2023-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35431.png

Downloads & links

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Map

FileDownload / File: emd_35431.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM map of the phage-encoded nucleus-like shell protein gp105 octahedral assembly reconstructed with O symmetry imposed (O map).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 400 pix.
= 500. Å		1.25 Å/pix.
x 400 pix.
= 500. Å		1.25 Å/pix.
x 400 pix.
= 500. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0725
Minimum - Maximum-0.0031405578 - 1.7539197
Average (Standard dev.)0.0034046224 (±0.039720956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 500.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The cryo-EM half map of the phage-encoded nucleus-like...

Fileemd_35431_half_map_1.map
AnnotationThe cryo-EM half map of the phage-encoded nucleus-like shell protein gp105 octahedral assembly reconstructed with O symmetry imposed (O map).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The cryo-EM half map of the phage-encoded nucleus-like...

Fileemd_35431_half_map_2.map
AnnotationThe cryo-EM half map of the phage-encoded nucleus-like shell protein gp105 octahedral assembly reconstructed with O symmetry imposed (O 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 gp105

EntireName: 201phi2-1 gp105
Components
  • Complex: 201phi2-1 gp105

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Supramolecule #1: 201phi2-1 gp105

SupramoleculeName: 201phi2-1 gp105 / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Pseudomonas phage 201phi2-1 (virus)

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134458
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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