+Open data
-Basic information
Entry | Database: PDB / ID: 6j3q | |||||||||||||||
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Title | Capsid structure of a freshwater cyanophage Siphoviridae Mic1 | |||||||||||||||
Components |
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Keywords | VIRUS / cyanophage / Siphoviridae / capsid | |||||||||||||||
Function / homology | Cement / Major capsid protein Function and homology information | |||||||||||||||
Biological species | Microcystis phage Mic1 (virus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å | |||||||||||||||
Authors | Jin, H. / Jiang, Y.L. / Yang, F. / Zhang, J.T. / Li, W.F. / Zhou, K. / Ju, J. / Chen, Y. / Zhou, C.Z. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Structure / Year: 2019 Title: Capsid Structure of a Freshwater Cyanophage Siphoviridae Mic1. Authors: Hua Jin / Yong-Liang Jiang / Feng Yang / Jun-Tao Zhang / Wei-Fang Li / Ke Zhou / Jue Ju / Yuxing Chen / Cong-Zhao Zhou / Abstract: Cyanobacteria are the most abundant photosynthetic microorganisms, the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in ...Cyanobacteria are the most abundant photosynthetic microorganisms, the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in the Lake Chaohu enabled us to isolate a freshwater siphocyanophage that infects Microcystis wesenbergii, thus termed Mic1. Using cryoelectron microscopy, we solved the 3.5-Å structure of Mic1 capsid. The major capsid protein gp40 of an HK97-like fold forms two types of capsomers, hexons and pentons. The capsomers interact with each other via the interweaved N-terminal arms of gp40 in addition to a tail-in-mouth joint along the three-fold symmetric axis, resulting in the assembly of capsid in a mortise-and-tenon pattern. The novel-fold cement protein gp47 sticks at the two-fold symmetric axis and further fixes the capsid. These findings provide structural insights into the assembly of cyanophages, and set up a platform to explore the mechanism of specific interactions and co-evolution with cyanobacteria. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6j3q.cif.gz | 916.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j3q.ent.gz | 780.4 KB | Display | PDB format |
PDBx/mmJSON format | 6j3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j3q_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6j3q_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6j3q_validation.xml.gz | 130.9 KB | Display | |
Data in CIF | 6j3q_validation.cif.gz | 206 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/6j3q ftp://data.pdbj.org/pub/pdb/validation_reports/j3/6j3q | HTTPS FTP |
-Related structure data
Related structure data | 9774MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 37879.035 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Microcystis phage Mic1 (virus) / References: UniProt: A0A4Y5TR23*PLUS #2: Protein | Mass: 10199.458 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Microcystis phage Mic1 (virus) / References: UniProt: A0A4Y5TPY8*PLUS |
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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: Cyanophage / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Microcystis phage Mic1 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Microcystis wesenbergii |
Virus shell | Name: gp40 / Diameter: 880 nm / Triangulation number (T number): 13 |
Buffer solution | pH: 7.5 / Details: 50 mM Tris-HCl pH7.5, 100 mM NaCl, 10 mM MgSO4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.76 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1935 |
Image scans | Movie frames/image: 32 |
-Processing
EM software |
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CTF correction | Details: CTFFIND4 / Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 18800 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9702 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |