1OHG

STRUCTURE OF THE DSDNA BACTERIOPHAGE HK97 MATURE EMPTY CAPSID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.373 
  • R-Value Observed: 0.373 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Refined Structure of a Protein Catenane: The Hk97 Bacteriophage Capsid at 3.44A Resolution

Helgstrand, C.Wikoff, W.R.Duda, R.L.Hendrix, R.W.Johnson, J.E.Liljas, L.

(2003) J Mol Biol 334: 885

  • DOI: 10.1016/j.jmb.2003.09.035
  • Primary Citation of Related Structures:  
    1OHG

  • PubMed Abstract: 
  • The HK97 bacteriophage capsid is a unique example of macromolecular catenanes: interlocked rings of covalently attached protein subunits. The chain mail organization of the subunits stabilizes a particle in which the maximum thickness of the protein shell is 18A and the maximum diameter is 550A ...

    The HK97 bacteriophage capsid is a unique example of macromolecular catenanes: interlocked rings of covalently attached protein subunits. The chain mail organization of the subunits stabilizes a particle in which the maximum thickness of the protein shell is 18A and the maximum diameter is 550A. The electron density has the appearance of a balloon illustrating the extraordinary strength conferred by the unique subunit organization. The refined structure shows novel qualities of the HK97 shell protein, gp5 that, together with the protease gp4, guides the assembly and maturation of the virion. Although gp5 forms hexamers and pentamers and the subunits exist in different structural environments, the tertiary structures of the seven protein molecules in the viral asymmetric unit are closely similar. The interactions of the subunits in the shell are exceptionally complex with each subunit interacting with nine other subunits. The interactions of the N-terminus released after gp5 cleavage appear important for organization of the loops that become crosslinked to the core of a neighboring subunit at the maturation. A comparison with a model of the Prohead II structure revealed that the surfaces of non-covalent contact between the monomers that build up hexamers/pentamers are completely redefined during maturation.


    Related Citations: 
    • Increased Resolution Data from a Large Unit Cell Crystal Collected at a Third-Generation Synchrotron X-Ray Source
      Wikoff, W.R., Schildkamp, W., Johnson, J.E.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 890
    • Topologically Linked Protein Rings in the Bacteriophage Hk97 Capsid
      Wikoff, W.R., Liljas, L., Duda, R.L., Tsuruta, H., Hendrix, R.W., Johnson, J.E.
      (2000) Science 289: 2129
    • Crystallographic Analysis of the DsDNA Bacteriophage Hk97 Mature Empty Capsid
      Wikoff, W.R., Duda, R.L., Hendrix, R.W., Johnson, J.E.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 763

    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR CAPSID PROTEINA, B, C, D, E, F, G282Escherichia virus HK97Mutation(s): 0 
Gene Names: 5
UniProt
Find proteins for P49861 (Enterobacteria phage HK97)
Explore P49861 
Go to UniProtKB:  P49861
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth G]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.374 
  • R-Value Work: 0.373 
  • R-Value Observed: 0.373 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 579.7α = 90
b = 626.65β = 89.9
c = 787.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-11
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Derived calculations, Other, Refinement description, Version format compliance