+Open data
-Basic information
Entry | Database: PDB / ID: 7kmx | ||||||
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Title | The capsid of Myoviridae Phage XM1 | ||||||
Components |
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Keywords | VIRUS / Myoviridae / Vibrio phage / Capsid / HK97 fold | ||||||
Biological species | Vibrio phage XM1 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Wang, Z. / Klose, T. / Jiang, W. / Kuhn, R.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biorxiv / Year: 2021 Title: Structure of Vibrio phage XM1, a simple contractile DNA injection machine Authors: Wang, Z. / Fokine, A. / Guo, X. / Jiang, W. / Rossmann, M.G. / Kuhn, R.J. / Luo, Z.H. / Klose, T. | ||||||
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 | 7kmx.cif.gz | 519 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kmx.ent.gz | 435.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kmx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7kmx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7kmx_validation.xml.gz | 92.6 KB | Display | |
Data in CIF | 7kmx_validation.cif.gz | 142.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/7kmx ftp://data.pdbj.org/pub/pdb/validation_reports/km/7kmx | HTTPS FTP |
-Related structure data
Related structure data | 22931MC 7kh1C 7kjkC 7klnC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 16823.863 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus) #2: Protein | Mass: 35512.773 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus) |
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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: Vibrio phage XM1 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Vibrio phage XM1 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Vibrio rotiferianus |
Virus shell | Name: capsid / Diameter: 640 nm / Triangulation number (T number): 7 |
Buffer solution | pH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19625 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |