PDBsum entry 2ft1

Go to PDB code: 
protein Protein-protein interface(s) links
Virus PDB id
Jmol PyMol
Protein chains
280 a.a. *
258 a.a. *
* Residue conservation analysis
PDB id:
Name: Virus
Title: Bacteriophage hk97 head ii
Structure: Major capsid protein. Chain: a, b, c, d, e, f, g. Synonym: gp5, head protein. Engineered: yes
Source: Enterobacteria phage hk97. Organism_taxid: 37554. Gene: 5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
3.90Å     R-factor:   0.297    
Authors: L.Gan,J.A.Speir,J.F.Conway,G.Lander,N.Cheng,B.A.Firek, R.W.Hendrix,R.L.Duda,L.Liljas,J.E.Johnson
Key ref:
L.Gan et al. (2006). Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM. Structure, 14, 1655-1665. PubMed id: 17098191 DOI: 10.1016/j.str.2006.09.006
23-Jan-06     Release date:   07-Feb-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P49861  (COAT_BPHK7) -  Major capsid protein
385 a.a.
280 a.a.
Protein chains
Pfam   ArchSchema ?
P49861  (COAT_BPHK7) -  Major capsid protein
385 a.a.
258 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1016/j.str.2006.09.006 Structure 14:1655-1665 (2006)
PubMed id: 17098191  
Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM.
L.Gan, J.A.Speir, J.F.Conway, G.Lander, N.Cheng, B.A.Firek, R.W.Hendrix, R.L.Duda, L.Liljas, J.E.Johnson.
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.
  Selected figure(s)  
Figure 1.
Figure 1. HK97 Capsid Expansion and Organization
(A) HK97 Prohead I is assembled in an expression system. Prohead II (PII) expands in vitro when perturbed by acidic pH (4.0) and changes through a series of discrete intermediates, acquiring progressively more crosslinks. Expansion Intermediates I and II (EI-I and EI-II) and all later particles, which have matured beyond the expansion checkpoint, will convert to the mature, fully crosslinked Head II (HII) upon neutralization. Particles can be expanded and trapped into specific intermediate states under defined acidification conditions. K169Y mutant procapsids follow a similar maturation trajectory, but they tend to remain as EI-II because they cannot crosslink (Ross et al., 2005). Fully expanded K169Y particles are called Head I (HI) and are similar to those of Head II, but they are not crosslinked; wild-type capsids do not convert to Head I before maturing to Head II.
(B) The HK97 mature capsid (Head II) is assembled from 420 capsid proteins that are organized as pentons (light green) and hexons (light blue). The T = 7 laevo lattice has icosahedral symmetry and is organized as 60 asymmetric units that each contain 7 gp5^* subunits. Icosahedral 5-fold (pentagon), 3-fold (triangle), and 2-fold (ellipse) axes are labeled. One icosahedral asymmetric unit, shown in dark colors, contains one whole hexon (A through F subunits) and one penton G subunit. The seven subunits are in chemically unique environments, but they adopt very similar conformations due to the high degree of quasi-equivalence.
(C) The ribbon model of one HK97 Head II gp5^* (C subunit) is colored by its four motifs: Domain A, teal; Domain P, gold; E loop, blue; and N arm, cyan. Two motifs that are described in detail in the text (spine helix and E loop β strands) are highlighted by light-blue rectangles. The 2 residues that form crosslinks (K169 and N356) are shown as red balls-and-sticks.
Figure 2.
Figure 2. Morphology of Expanded Capsid States
The structure of EI-IV determined by cryo-EM to 12 Å resolution and the structures of EI-IV, pepEI-IV, K169Y Head I, and Head II determined by X-ray crystallography to 7.5, 3.8, 4.2, and 3.9 Å resolution, respectively. Left to right: (1) SDS-PAGE lanes of the purified particles. EI-IV and pepEI-IV particles have predominantly closed 5-mers (top-most band) and open 6-mers (thick band). Closed 5-mers are formed by five crosslinked hexon subunits that surround a penton, and open 6-mers are formed by five hexon subunits and one penton subunit that surround a hexon. Head II has all possible crosslinks (420), which interlock the capsid subunits into a unitary chainmail structure that is retained in the stacking gel. K169Y Head I subunits cannot crosslink, and they therefore run as monomers. (2) Schematic of the organization of intersubunit crosslinks for the capsid states. One penton (dark shade) is shown with its surrounding hexons (light shade). Subunits are represented by ovals, and crosslinks are represented by lines. The last class of crosslink (red) forms between a penton (G) and a hexon (F) subunit. These crosslinks are represented by a dotted line for EI-IV, where they are not yet formed, and for pepEI-IV, where they cannot form. Crosslinks are completely absent in the mutant K169Y Head I particles. (3) Electron density maps of EI-IV determined by cryo-EM at 12 Å resolution and of the other capsid states determined by X-ray crystallography, but restricted to 7.5 Å resolution. All maps are contoured at 1.5σ, except for the crystal structure of EI-IV, which is contoured at 0.5σ in order to show the finger-like structure (see below). The region around a penton is boxed in red, dotted lines and is magnified in the images on the right. (4) Stereo images of the penton boxed in (3) and rendered at the resolution limit of the structure. In the stereo image of the EI-IV penton determined by X-ray crystallography, the red arrows point to the poorly ordered, finger-like structure formed by residues 159–171. This structure is not present in any of the other maps.
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1655-1665) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21276801 R.K.Huang, R.Khayat, K.K.Lee, I.Gertsman, R.L.Duda, R.W.Hendrix, and J.E.Johnson (2011).
The Prohead-I structure of bacteriophage HK97: implications for scaffold-mediated control of particle assembly and maturation.
  J Mol Biol, 408, 541-554.
PDB code: 3qpr
20093122 I.Gertsman, E.A.Komives, and J.E.Johnson (2010).
HK97 maturation studied by crystallography and H/2H exchange reveals the structural basis for exothermic particle transitions.
  J Mol Biol, 397, 560-574.  
20149636 J.E.Johnson (2010).
Virus particle maturation: insights into elegantly programmed nanomachines.
  Curr Opin Struct Biol, 20, 210-216.  
18983851 D.Nemecek, S.A.Overman, R.W.Hendrix, and G.J.Thomas (2009).
Unfolding thermodynamics of the Delta-domain in the prohead I subunit of phage HK97: determination by factor analysis of Raman spectra.
  J Mol Biol, 385, 628-641.  
19204733 I.Gertsman, L.Gan, M.Guttman, K.Lee, J.A.Speir, R.L.Duda, R.W.Hendrix, E.A.Komives, and J.E.Johnson (2009).
An unexpected twist in viral capsid maturation.
  Nature, 458, 646-650.
PDB code: 3e8k
19091865 L.E.Dierkes, C.L.Peebles, B.A.Firek, R.W.Hendrix, and R.L.Duda (2009).
Mutational analysis of a conserved glutamic acid required for self-catalyzed cross-linking of bacteriophage HK97 capsids.
  J Virol, 83, 2088-2098.  
19540242 R.L.Duda, P.D.Ross, N.Cheng, B.A.Firek, R.W.Hendrix, J.F.Conway, and A.C.Steven (2009).
Structure and energetics of encapsidated DNA in bacteriophage HK97 studied by scanning calorimetry and cryo-electron microscopy.
  J Mol Biol, 391, 471-483.  
18786402 G.C.Lander, A.Evilevitch, M.Jeembaeva, C.S.Potter, B.Carragher, and J.E.Johnson (2008).
Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM.
  Structure, 16, 1399-1406.  
18940605 K.K.Lee, L.Gan, H.Tsuruta, C.Moyer, J.F.Conway, R.L.Duda, R.W.Hendrix, A.C.Steven, and J.E.Johnson (2008).
Virus capsid expansion driven by the capture of mobile surface loops.
  Structure, 16, 1491-1502.
PDB code: 3ddx
18421144 L.Gan, and J.E.Johnson (2008).
An optimal exposure strategy for cryoprotected virus crystals with lattice constants greater than 1000 A.
  J Synchrotron Radiat, 15, 223-226.  
18498137 V.L.Morton, P.G.Stockley, N.J.Stonehouse, and A.E.Ashcroft (2008).
Insights into virus capsid assembly from non-covalent mass spectrometry.
  Mass Spectrom Rev, 27, 575-595.  
18423102 E.Nurmemmedov, M.Castelnovo, C.E.Catalano, and A.Evilevitch (2007).
Biophysics of viral infectivity: matching genome length with capsid size.
  Q Rev Biophys, 40, 327-356.  
17680786 K.N.Parent, M.M.Suhanovsky, and C.M.Teschke (2007).
Polyhead formation in phage P22 pinpoints a region in coat protein required for conformational switching.
  Mol Microbiol, 65, 1300-1310.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.