+Open data
-Basic information
Entry | Database: PDB / ID: 6ibc | |||||||||||||||||||||
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Title | Thermophage P23-45 procapsid | |||||||||||||||||||||
Components | Major head protein | |||||||||||||||||||||
Keywords | VIRUS / bacteriophage / thermophage / caudovirales / siphoviridae / capsid / procapsid / auxiliary / HK97 | |||||||||||||||||||||
Function / homology | Major capsid protein GpE / Phage major capsid protein E / T=7 icosahedral viral capsid / host cell cytoplasm / Major capsid protein Function and homology information | |||||||||||||||||||||
Biological species | Thermus virus P23-45 | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.39 Å | |||||||||||||||||||||
Authors | Bayfield, O.W. / Klimuk, E. / Winkler, D.C. / Hesketh, E.L. / Chechik, M. / Cheng, N. / Dykeman, E.C. / Minakhin, L. / Ranson, N.A. / Severinov, K. ...Bayfield, O.W. / Klimuk, E. / Winkler, D.C. / Hesketh, E.L. / Chechik, M. / Cheng, N. / Dykeman, E.C. / Minakhin, L. / Ranson, N.A. / Severinov, K. / Steven, A.C. / Antson, A.A. | |||||||||||||||||||||
Funding support | United Kingdom, United States, Russian Federation, 6items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. Authors: Oliver W Bayfield / Evgeny Klimuk / Dennis C Winkler / Emma L Hesketh / Maria Chechik / Naiqian Cheng / Eric C Dykeman / Leonid Minakhin / Neil A Ranson / Konstantin Severinov / Alasdair C ...Authors: Oliver W Bayfield / Evgeny Klimuk / Dennis C Winkler / Emma L Hesketh / Maria Chechik / Naiqian Cheng / Eric C Dykeman / Leonid Minakhin / Neil A Ranson / Konstantin Severinov / Alasdair C Steven / Alfred A Antson / Abstract: Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic ...Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside. | |||||||||||||||||||||
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 | 6ibc.cif.gz | 444.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ibc.ent.gz | 365.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ibc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ibc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ibc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ibc_validation.xml.gz | 81.8 KB | Display | |
Data in CIF | 6ibc_validation.cif.gz | 123.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/6ibc ftp://data.pdbj.org/pub/pdb/validation_reports/ib/6ibc | HTTPS FTP |
-Related structure data
Related structure data | 4447MC 4433C 4445C 4446C 6i9eC 6ibgC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
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-Components
#1: Protein | Mass: 46680.754 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Thermus virus P23-45 / Cell line: Thermus thermophilus HB8 / References: UniProt: A7XXC2 |
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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: Thermus phage P2345 / Type: VIRUS / Entity ID: all / Source: NATURAL | ||||||||||||||||
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Molecular weight | Value: 19.58 MDa / Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Thermus phage P2345 (virus) | ||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION | ||||||||||||||||
Natural host | Organism: Thermus thermophilus HB8 | ||||||||||||||||
Virus shell | Triangulation number (T number): 7 | ||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 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: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2 sec. / Electron dose: 99 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38044 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||
Refinement | Highest resolution: 4.39 Å | |||||||||||||||||||||||||||
Refine LS restraints |
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