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Yorodumi- PDB-6ibg: Bacteriophage G20c portal protein crystal structure for construct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ibg | |||||||||||||||||||||
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Title | Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus | |||||||||||||||||||||
Components | Portal protein | |||||||||||||||||||||
Keywords | VIRAL PROTEIN / bacteriophage / thermophage / caudovirales / siphoviridae / capsid / auxiliary / HK97 / virus | |||||||||||||||||||||
Function / homology | viral capsid / Portal protein Function and homology information | |||||||||||||||||||||
Biological species | Thermus virus P23-45 | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ibg.cif.gz | 518.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ibg.ent.gz | 429.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ibg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ibg_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 6ibg_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 6ibg_validation.xml.gz | 47.5 KB | Display | |
Data in CIF | 6ibg_validation.cif.gz | 68.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/6ibg ftp://data.pdbj.org/pub/pdb/validation_reports/ib/6ibg | HTTPS FTP |
-Related structure data
Related structure data | 4433C 4445C 4446C 4447C 6i9eC 6ibcC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 49388.648 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus virus P23-45 / Gene: P23p86 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7XXB9 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 13.3mg/ml protein, 2mg/ml 42-amino acid peptide kdgykfelaeerpsklkheesvmslveddftdlelanrafsa, 20 mM Tris-HCl pH 7.5, 1 M NaCl, 5 % v/v glycerol. Reservoir: 40 % MPD v/v, 200 mM NaH2PO4 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→94.2 Å / Num. obs: 105514 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Net I/av σ(I): 6.2 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 7 % / Rmerge(I) obs: 1.199 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7752 / CC1/2: 0.626 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 1.95→10 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.818 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.453 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→10 Å
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Refine LS restraints |
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