Bacteriophage HK97 Expansion Intermediate IV

Experimental Data Snapshot

  • Resolution: 7.50 Å
  • R-Value Work: 0.421 
  • R-Value Observed: 0.421 

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Capsid Conformational Sampling in HK97 Maturation Visualized by X-Ray Crystallography and Cryo-EM.

Gan, L.Speir, J.A.Conway, J.F.Lander, G.Cheng, N.Firek, B.A.Hendrix, R.W.Duda, R.L.Liljas, L.Johnson, J.E.

(2006) Structure 14: 1655-1665

  • DOI: https://doi.org/10.1016/j.str.2006.09.006
  • Primary Citation of Related Structures:  
    2FRP, 2FS3, 2FSY, 2FT1, 2FTE

  • PubMed Abstract: 

    Maturation of the bacteriophage HK97 capsid from a precursor (Prohead II) to the mature state (Head II) involves a 60 A radial expansion. The mature particle is formed by 420 copies of the major capsid protein organized on a T = 7 laevo lattice with each subunit covalently crosslinked to two neighbors. Well-characterized pH 4 expansion intermediates make HK97 valuable for investigating quaternary structural dynamics. Here, we use X-ray crystallography and cryo-EM to demonstrate that in the final transition in maturation (requiring neutral pH), pentons in Expansion Intermediate IV (EI-IV) reversibly sample 14 A translations and 6 degrees rotations relative to a fixed hexon lattice. The limit of this trajectory corresponds to the Head II conformation that is secured at this extent only by the formation of the final class of covalent crosslinks. Mutants that cannot crosslink or EI-IV particles that have been rendered incapable of forming the final crosslink remain in the EI-IV state.

  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A, B, C, D, E
A, B, C, D, E, F, G
282Byrnievirus HK97Mutation(s): 0 
Gene Names: 5
Find proteins for P49861 (Enterobacteria phage HK97)
Explore P49861 
Go to UniProtKB:  P49861
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49861
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 7.50 Å
  • R-Value Work: 0.421 
  • R-Value Observed: 0.421 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 1008.967α = 90
b = 1008.967β = 90
c = 728.638γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2023-09-20
    Changes: Data collection, Refinement description