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

PDB 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.

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

PubMed: 14643655 Search on PubMed
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.

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) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR CAPSID PROTEIN	A, B, C, D, E, F, G 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49861
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth G] MOL2 format, chain I [auth G]	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 = 579.7	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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2003-05-26
Released Date: 2003-12-11

Deposition Author(s):

This entry supersedes: 1FH6

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