Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 420-mer - A420 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 215.76 kDa 
• Atom Count: 15070 
• Modelled Residue Count: 1967 
• Deposited Residue Count: 1974 
• Unique protein chains: 1

1OHG

STRUCTURE OF THE DSDNA BACTERIOPHAGE HK97 MATURE EMPTY CAPSID

• DOI: 10.2210/pdb1OHG/pdb
• Entry: 1OHG supersedes: 1FH6

• Classification: VIRUS
• Organism(s): Escherichia virus HK97
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-05-26 Released: 2003-12-11 
• Deposition Author(s): Helgstrand, C., Wikoff, W.R., Duda, R.L., Hendrix, R.W., Johnson, J.E., Liljas, L.

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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 

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: 14643655 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR CAPSID PROTEIN	A, B, C, D, E, F, G	282	Escherichia virus HK97	Mutation(s): 0  Gene Names: 5
UniProt
Find proteins for P49861 (Enterobacteria phage HK97) Explore P49861  Go to UniProtKB:  P49861

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	I [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 579.7	α = 90
b = 626.65	β = 89.9
c = 787.2	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-26 
• Released Date: 2003-12-11 
Deposition Author(s): Helgstrand, C., Wikoff, W.R., Duda, R.L., Hendrix, R.W., Johnson, J.E., Liljas, L.
• This entry supersedes: 1FH6

Revision History  

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