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 

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


  • 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 ...

    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: 
    • 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
    • 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.,Sect.D 56: 890
    • 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.,Sect.D 55: 763

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR CAPSID PROTEIN
A, B, C, D, E, F, G
282Enterobacteria phage HK97Mutation(s): 0 
Gene Names: 5
Find proteins for P49861 (Enterobacteria phage HK97)
Go to UniProtKB:  P49861
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 579.700α = 90.00
b = 626.650β = 89.90
c = 787.200γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AVEphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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