3QPR

HK97 Prohead I encapsidating inactive virally encoded protease

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.20 Å
  • R-Value Free: 0.467 
  • R-Value Work: 0.461 
  • R-Value Observed: 0.461 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The Prohead-I structure of bacteriophage HK97: implications for scaffold-mediated control of particle assembly and maturation.

Huang, R.K., Khayat, R., Lee, K.K., Gertsman, I., Duda, R.L., Hendrix, R.W., Johnson, J.E.

(2011) J Mol Biol 408: 541-554

  • DOI: 10.1016/j.jmb.2011.01.016
  • Primary Citation of Related Structures:  
    3QPR

  • PubMed Abstract: 

    • Virus capsid assembly requires recruiting and organizing multiple copies of protein subunits to form a closed shell for genome packaging that leads to infectivity. Many viruses encode scaffolding proteins to shift the equilibrium toward particle formation by promoting intersubunit interactions and stabilizing assembly intermediates ...

    Virus capsid assembly requires recruiting and organizing multiple copies of protein subunits to form a closed shell for genome packaging that leads to infectivity. Many viruses encode scaffolding proteins to shift the equilibrium toward particle formation by promoting intersubunit interactions and stabilizing assembly intermediates. Bacteriophage HK97 lacks an explicit scaffolding protein, but the capsid protein (gp5) contains a scaffold-like N-terminal segment termed the delta domain. When gp5 is expressed in Escherichia coli, the delta domain guides 420 copies of the subunit into a procapsid with T=7 laevo icosahedral symmetry named Prohead-I. Prohead-I can be disassembled and reassembled under mild conditions and it cannot mature further. When the virally encoded protease (gp4) is coexpressed with gp5, it is incorporated into the capsid and digests the delta domain followed by autoproteolysis to produce the metastable Prohead-II. Prohead-I(+P) was isolated by coexpressing gp5 and an inactive mutant of gp4. Prohead-I and Prohead-I(+P) were compared by biochemical methods, revealing that the inactive protease stabilized the capsid against disassembly by chemical or physical stress. The crystal structure of Prohead-I(+P) was determined at 5.2 Å resolution, and distortions were observed in the subunit tertiary structures similar to those observed previously in Prohead-II. Prohead-I(+P) differed from Prohead-II due to the presence of the delta domain and the resulting repositioning of the N-arms, explaining why Prohead-I can be reversibly dissociated and cannot mature. Low-resolution X-ray data enhanced the density of the relatively dynamic delta domains, revealing their quaternary arrangement and suggesting how they drive proper assembly.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein
A, B, C, D, E, F, G
A, B, C, D, E, F, G
385Escherichia virus HK97Mutation(s): 0 
Gene Names: 5
UniProt
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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.20 Å
  • R-Value Free: 0.467 
  • R-Value Work: 0.461 
  • R-Value Observed: 0.461 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 560.12α = 90
b = 560.12β = 90
c = 560.12γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
RAVEmodel building
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
RAVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Derived calculations
  • Version 1.3: 2013-01-30
    Changes: Other