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

Basic information

Entry

Database: EMDB / ID: EMD-35431

• Title: 201Phi2-1 gp105 cube-like assembly (O, 24mer)
• Map data: The 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 species: Pseudomonas phage 201phi2-1 (virus)
• Method: single particle reconstruction / cryo EM / Resolution: 4.76 Å
• Authors: Liu Z / Xiang Y

Funding support

China, 1 items

Organization	Grant number	Country
Ministry of Science and Technology (MoST, China)	2021YFA1300204	China

• Citation: Journal: 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 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

Deposition	Feb 20, 2023	-
Header (metadata) release	May 3, 2023	-
Map release	May 3, 2023	-
Update	May 24, 2023	-
Current status	May 24, 2023	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_35431.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: The cryo-EM map of the phage-encoded nucleus-like shell protein gp105 octahedral assembly reconstructed with O symmetry imposed (O map).
• Voxel size: X=Y=Z: 1.25 Å

Density

Contour Level	By AUTHOR: 0.0725
Minimum - Maximum	-0.0031405578 - 1.7539197
Average (Standard dev.)	0.0034046224 (±0.039720956)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 500.0 Å α=β=γ: 90.0 °

Supplemental data

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

• File: emd_35431_half_map_1.map
• Annotation: The cryo-EM half map of the phage-encoded nucleus-like shell protein gp105 octahedral assembly reconstructed with O symmetry imposed (O map).

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

• File: emd_35431_half_map_2.map
• Annotation: The cryo-EM half map of the phage-encoded nucleus-like shell protein gp105 octahedral assembly reconstructed with O symmetry imposed (O map).

Sample components

Entire : 201phi2-1 gp105

• Entire: Name: 201phi2-1 gp105

Components

• Complex: 201phi2-1 gp105

Supramolecule #1: 201phi2-1 gp105

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

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134458