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Yorodumi- PDB-5wk1: Structure of the major capsid protein and the capsid stabilizing ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wk1 | ||||||
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Title | Structure of the major capsid protein and the capsid stabilizing protein of the marine siphovirus TW1 | ||||||
Components |
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Keywords | VIRUS / Major Capsid Protein / Capsid Stabilizing Protein / HK 97 fold / Decoration Protein | ||||||
Function / homology | viral capsid / Putative coat protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudoalteromonas phage TW1 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Wang, Z. / Rossmann, M.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2018 Title: Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes. Authors: Zhiqing Wang / Stephen C Hardies / Andrei Fokine / Thomas Klose / Wen Jiang / Byung Cheol Cho / Michael G Rossmann / Abstract: Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of ...Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of most of these proteins have been predicted by bioinformatic methods. A 3.6 Å resolution cryoelectron microscopy map of the icosahedrally averaged TW1 head showed the atomic structures of the major capsid protein, gp57, and the capsid-stabilizing protein, gp56. The gp57 structure is similar to that of the phage HK97 capsid protein. The gp56 protein has two domains, each having folds similar to that of the N-terminal part of phage λ gpD, indicating a common ancestry. The first gp56 domain clamps adjacent capsomers together, whereas the second domain is required for trimerization. A 6-fold-averaged reconstruction of the distal part of the tail showed that TW1 has six tail spikes, which are unusual for siphophages but are similar to the podophages P22 and Sf6, suggesting a common evolutionary origin of these spikes. | ||||||
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 | 5wk1.cif.gz | 507.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wk1.ent.gz | 423.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wk1_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5wk1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5wk1_validation.xml.gz | 86 KB | Display | |
Data in CIF | 5wk1_validation.cif.gz | 119.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wk1 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wk1 | HTTPS FTP |
-Related structure data
Related structure data | 8854MC 7070C 8867C 8868C 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: 15017.777 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas phage TW1 (virus) / References: UniProt: S5MS27 #2: Protein | Mass: 39047.965 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas phage TW1 (virus) / References: UniProt: S5M825 |
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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: Pseudoalteromonas phage TW1 / Type: VIRUS / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Source (natural) | Organism: Pseudoalteromonas phage TW1 (virus) | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid mesh size: 400 divisions/in. / Grid type: Ted Pella Inc, Lacey Carbon | ||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 75 % / 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 magnification: 22500 X / 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 / Temperature (max): 80 K / Temperature (min): 80 K |
Image recording | Electron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 16216 | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8663 / Symmetry type: POINT |