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Yorodumi- PDB-8igg: C2 reconstruction of the concave tetramer in the cube-like assemb... -
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-Basic information
Entry | Database: PDB / ID: 8igg | ||||||
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Title | C2 reconstruction of the concave tetramer in the cube-like assembly of 201Phi2-1 gp105 | ||||||
Components | Chimallin | ||||||
Keywords | STRUCTURAL PROTEIN / jumbo phage 201phi2-1 / gp105 / nucleus-like structure. | ||||||
Function / homology | host cell cytoplasm / Chimallin Function and homology information | ||||||
Biological species | Pseudomonas phage 201phi2-1 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.09 Å | ||||||
Authors | Liu, Z. / Xiang, Y. | ||||||
Funding support | China, 1items
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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 ...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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8igg.cif.gz | 350.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8igg.ent.gz | 289.9 KB | Display | PDB format |
PDBx/mmJSON format | 8igg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/8igg ftp://data.pdbj.org/pub/pdb/validation_reports/ig/8igg | HTTPS FTP |
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-Related structure data
Related structure data | 35432MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 70654.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage 201phi2-1 (virus) / Gene: 201phi2-1p105 / Production host: Escherichia coli (E. coli) / References: UniProt: B3FIW8 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 201Phi2-1 gp105 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Pseudomonas phage 201phi2-1 (virus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 290996 / Num. of class averages: 1 / Symmetry type: POINT |