+Open data
-Basic information
Entry | Database: PDB / ID: 7f38 | ||||||
---|---|---|---|---|---|---|---|
Title | Cyanophage A-1(L) capsid asymmetric unit | ||||||
Components | Putative major capsid protein | ||||||
Keywords | VIRUS / Major capsid proteins | ||||||
Function / homology | Putative major capsid protein Function and homology information | ||||||
Biological species | Nostoc phage A1 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å | ||||||
Authors | Cui, N. / Li, Q. / Zhou, C.Z. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: J Virol / Year: 2021 Title: Capsid Structure of Cyanophage A-1(L). Authors: Ning Cui / Feng Yang / Jun-Tao Zhang / Hui Sun / Yu Chen / Rong-Cheng Yu / Zhi-Peng Chen / Yong-Liang Jiang / Shu-Jing Han / Xudong Xu / Qiong Li / Cong-Zhao Zhou / Abstract: A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a ...A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a century, its structure remains unknown, which limits our understanding on the interplay between A-1(L) and its host. Here we report the 3.35 Å cryo-EM structure of A-1(L) capsid, representing the first near-atomic resolution structure of a phage capsid with a T number of 9. The major capsid gp4 proteins assemble into 91 capsomers, including 80 hexons: 20 at the center of the facet and 60 at the facet edge, in addition to 11 identical pentons. These capsomers further assemble into the icosahedral capsid, via gradually increasing curvatures. Different from the previously reported capsids of known-structure, A-1(L) adopts a noncovalent chainmail structure of capsid stabilized by two kinds of mortise-and-tenon inter-capsomer interactions: a three-layered interface at the pseudo 3-fold axis combined with the complementarity in shape and electrostatic potential around the 2-fold axis. This unique capsomer construction enables A-1(L) to possess a rigid capsid, which is solely composed of the major capsid proteins with an HK97 fold. Cyanobacteria are the most abundant photosynthetic bacteria, contributing significantly to the biomass production, O generation, and CO consumption on our planet. Their community structure and homeostasis in natural aquatic ecosystems are largely regulated by the corresponding cyanophages. In this study, we solved the structure of cyanophage A-1(L) capsid at near-atomic resolution and revealed a unique capsid construction. This capsid structure provides the molecular details for better understanding the assembly of A-1(L), and a structural platform for future investigation and application of A-1(L) in combination with its host sp. PCC 7120. As the first isolated freshwater cyanophage that infects the genetically tractable model cyanobacterium, A-1(L) should become an ideal template for the genetic engineering and synthetic biology studies. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7f38.cif.gz | 528.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7f38.ent.gz | 447.2 KB | Display | PDB format |
PDBx/mmJSON format | 7f38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f38_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7f38_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7f38_validation.xml.gz | 102.5 KB | Display | |
Data in CIF | 7f38_validation.cif.gz | 150 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/7f38 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/7f38 | HTTPS FTP |
-Related structure data
Related structure data | 31431MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 39524.617 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc phage A1 (virus) / Production host: Nostoc phage A1 (virus) / References: UniProt: A0A191SAV5 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Nostoc phage A1 / Type: VIRUS / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Nostoc phage A1 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Nostoc sp. PCC 7120 = FACHB-418 |
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
---|---|
3D reconstruction | Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32687 / Symmetry type: POINT |