The crystal structure of head fiber gp8.5 N base in bacteriophage phi29

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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This is version 2.1 of the entry. See complete history


Structural assembly of the tailed bacteriophage φ29.

Xu, J.Wang, D.Gui, M.Xiang, Y.

(2019) Nat Commun 10: 2366-2366

  • DOI: https://doi.org/10.1038/s41467-019-10272-3
  • Primary Citation of Related Structures:  
    6QVK, 6QX7, 6QYD, 6QYJ, 6QYM, 6QYY, 6QYZ, 6QZ0, 6QZ9, 6QZF

  • PubMed Abstract: 

    The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.

  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid fiber protein
A, B, C, D, E
A, B, C, D, E, F
119Salasvirus phi29Mutation(s): 0 
Gene Names: 8.5
Find proteins for B3VMP4 (Bacillus phage phi29)
Explore B3VMP4 
Go to UniProtKB:  B3VMP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3VMP4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.212α = 90
b = 65.07β = 99.09
c = 118.874γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0501100
Ministry of Science and Technology (China)China2015CB910102
National Natural Science Foundation of ChinaChina31470721

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-05-15
    Changes: Data collection, Database references