Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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This is version 1.5 of the entry. See complete history


Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.

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.

(2019) Proc Natl Acad Sci U S A 116: 3556-3561

  • DOI: https://doi.org/10.1073/pnas.1813204116
  • Primary Citation of Related Structures:  
    6I9E, 6IBC, 6IBG

  • PubMed 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 understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Thermus thermophilus 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.

  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein
A, B, C
446Oshimavirus P2345Mutation(s): 0 
Gene Names: P23p86
Find proteins for A7XXB9 (Thermus virus P23-45)
Explore A7XXB9 
Go to UniProtKB:  A7XXB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7XXB9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.081α = 90
b = 159.081β = 90
c = 116.913γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom206377
Wellcome TrustUnited Kingdom103460
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States--
Russian Foundation for Basic ResearchRussian Federation16-34-60137
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L021250/1
Wellcome TrustUnited Kingdom108466

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-30
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.5: 2024-06-19
    Changes: Data collection, Refinement description