Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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: 215.87 kDa 
• Atom Count: 14664 
• Modelled Residue Count: 1901 
• Deposited Residue Count: 1974 
• Unique protein chains: 1

2FS3

Bacteriophage HK97 K169Y Head I

• PDB DOI: 10.2210/pdb2FS3/pdb

• Classification: VIRUS
• Organism(s): Escherichia virus HK97
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-01-20 Released: 2006-02-07 
• Deposition Author(s): Gan, L., Speir, J.A., Conway, J.F., Lander, G., Cheng, N., Firek, B.A., Hendrix, R.W., Duda, R.L., Liljas, L., Johnson, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Work: 0.384 
• R-Value Observed: 0.384 

Literature

Capsid Conformational Sampling in HK97 Maturation Visualized by X-Ray Crystallography and Cryo-EM.

Gan, L., Speir, J.A., Conway, J.F., Lander, G., Cheng, N., Firek, B.A., Hendrix, R.W., Duda, R.L., Liljas, L., Johnson, J.E.

(2006) Structure 14: 1655-1665

• PubMed: 17098191 
• DOI: 10.1016/j.str.2006.09.006
• Primary Citation of Related Structures:  
  2FRP, 2FS3, 2FSY, 2FT1, 2FTE


• PubMed Abstract: 
  

Maturation of the bacteriophage HK97 capsid from a precursor (Prohead II) to the mature state (Head II) involves a 60 A radial expansion. The mature particle is formed by 420 copies of the major capsid protein organized on a T = 7 laevo lattice with each subunit covalently crosslinked to two neighbors. Well-characterized pH 4 expansion intermediates make HK97 valuable for investigating quaternary structural dynamics. Here, we use X-ray crystallography and cryo-EM to demonstrate that in the final transition in maturation (requiring neutral pH), pentons in Expansion Intermediate IV (EI-IV) reversibly sample 14 A translations and 6 degrees rotations relative to a fixed hexon lattice. The limit of this trajectory corresponds to the Head II conformation that is secured at this extent only by the formation of the final class of covalent crosslinks. Mutants that cannot crosslink or EI-IV particles that have been rendered incapable of forming the final crosslink remain in the EI-IV state.

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Organizational Affiliation: 

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

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): 1  Gene Names: 5
UniProt
Find proteins for P49861 (Enterobacteria phage HK97) Explore P49861  Go to UniProtKB:  P49861

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Work: 0.384 
• R-Value Observed: 0.384 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 1009.643	α = 90
b = 1009.643	β = 90
c = 729.812	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
RAVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-20 
• Released Date: 2006-02-07 
Deposition Author(s): Gan, L., Speir, J.A., Conway, J.F., Lander, G., Cheng, N., Firek, B.A., Hendrix, R.W., Duda, R.L., Liljas, L., Johnson, J.E.

Revision History  

• Version 1.0: 2006-02-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references