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PDBsum entry 1cd3
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protein Protein-protein interface(s) links
Virus PDB id
1cd3

 

 

 

 

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Contents
Protein chains
143 a.a. *
135 a.a. *
426 a.a. *
175 a.a. *
68 a.a. *
Waters ×96
* Residue conservation analysis
PDB id:
1cd3
Name: Virus
Title: Procapsid of bacteriophage phix174
Structure: Protein (scaffolding protein gpd). Chain: 1, 2, 3, 4. Protein (capsid protein gpf). Chain: f. Protein (spike protein gpg). Chain: g. Protein (scaffolding protein gpb). Chain: b
Source: Enterobacteria phage phix174. Organism_taxid: 10847. Strain: c. Strain: c
Resolution:
3.50Å     R-factor:   0.275    
Authors: M.G.Rossmann,T.Dokland
Key ref:
T.Dokland et al. (1999). The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174. J Mol Biol, 288, 595-608. PubMed id: 10329166 DOI: 10.1006/jmbi.1999.2699
Date:
05-Mar-99     Release date:   14-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P69486  (SCAFD_BPPHS) -  External scaffolding protein D from Enterobacteria phage phiX174
Seq:
Struc: 		152 a.a.
143 a.a.
Protein chains
P69486  (SCAFD_BPPHS) -  External scaffolding protein D from Enterobacteria phage phiX174
Seq:
Struc: 		152 a.a.
135 a.a.
Protein chain
P03641  (CAPSD_BPPHS) -  Capsid protein F from Enterobacteria phage phiX174
Seq:
Struc: 		427 a.a.
426 a.a.*
Protein chain
P03643  (G_BPPHS) -  Major spike protein G from Enterobacteria phage phiX174
Seq:
Struc: 		175 a.a.
175 a.a.
Protein chain
P03633  (SCAFB_BPPHS) -  Internal scaffolding protein B from Enterobacteria phage phiX174
Seq:
Struc: 		120 a.a.
68 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 10 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain B: E.C.3.4.-.-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1006/jmbi.1999.2699 J Mol Biol 288:595-608 (1999)
PubMed id: 10329166  
 
 
The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174.
T.Dokland, R.A.Bernal, A.Burch, S.Pletnev, B.A.Fane, M.G.Rossmann.
 
  ABSTRACT  
 
An empty precursor particle called the procapsid is formed during assembly of the single-stranded DNA bacteriophage phiX174. Assembly of the phiX174 procapsid requires the presence of the two scaffolding proteins, D and B, which are structural components of the procapsid, but are not found in the mature virion. The X-ray crystallographic structure of a "closed" procapsid particle has been determined to 3.5 A resolution. This structure has an external scaffold made from 240 copies of protein D, 60 copies of the internally located B protein, and contains 60 copies of each of the viral structural proteins F and G, which comprise the shell and the 5-fold spikes, respectively. The F capsid protein has a similar conformation to that seen in the mature virion, and differs from the previously determined 25 A resolution electron microscopic reconstruction of the "open" procapsid, in which the F protein has a different conformation. The D scaffolding protein has a predominantly alpha-helical fold and displays remarkable conformational variability. We report here an improved and refined structure of the closed procapsid and describe in some detail the differences between the four independent D scaffolding proteins per icosahedral asymmetric unit, as well as their interaction with the F capsid protein. We re-analyze and correct the comparison of the closed procapsid with the previously determined cryo-electron microscopic image reconstruction of the open procapsid and discuss the major structural rearrangements that must occur during assembly. A model is proposed in which the D proteins direct the assembly process by sequential binding and conformational switching.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo representation of the helical domain of the C a back- bone of the F protein in the procap- sid structure (red) and the F protein in the virion (black). The superimposed b-barrel domain is colored green in the procapsid structure and blue in the virion. Symmetry axes are those in the virion. 		Figure 9.
Figure 9. View down the 3-fold axis showing the relationship of the F protein as seen in the closed procapsid when superimposed onto the EM density of the open procapsid. The big hole on the 3-fold axis in the EM reconstruc- tion of the open procapsid is covered by helix 4 of the F protein in the closed procapsid X-ray structure. Gray and blue contours represent two density levels in the 25 Å resolution EM structure.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 288, 595-608) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19726536 D.R.Rokyta, and H.A.Wichman (2009).
Genic incompatibilities in two hybrid bacteriophages.
  Mol Biol Evol, 26, 2831-2839.  
19474099 J.E.Cherwa, and B.A.Fane (2009).
Complete virion assembly with scaffolding proteins altered in the ability to perform a critical conformational switch.
  J Virol, 83, 7391-7396.  
19726521 J.E.Cherwa, P.Sanchez-Soria, H.A.Wichman, B.A.Fane, J.A.Birkholz, H.A.Dineen, D.C.Grippi, T.L.Kempton, J.Kwan, N.N.Patel, P.Sanchez-Soria, and B.M.Toussaint (2009).
Viral adaptation to an antiviral protein enhances the fitness level to above that of the uninhibited wild type.
  J Virol, 83, 11746-11750.  
18400861 J.E.Cherwa, A.Uchiyama, and B.A.Fane (2008).
Scaffolding proteins altered in the ability to perform a conformational switch confer dominant lethal assembly defects.
  J Virol, 82, 5774-5780.  
17553892 A.Uchiyama, M.Chen, and B.A.Fane (2007).
Characterization and function of putative substrate specificity domain in microvirus external scaffolding proteins.
  J Virol, 81, 8587-8592.  
16428417 D.R.Rokyta, C.L.Burch, S.B.Caudle, and H.A.Wichman (2006).
Horizontal gene transfer and the evolution of microvirid coliphage genomes.
  J Bacteriol, 188, 1134-1142.  
16361237 K.M.Pepin, M.A.Samuel, and H.A.Wichman (2006).
Variable pleiotropic effects from mutations at the same locus hamper prediction of fitness from a fitness component.
  Genetics, 172, 2047-2056.  
16756387 M.De Paepe, and F.Taddei (2006).
Viruses' life history: towards a mechanistic basis of a trade-off between survival and reproduction among phages.
  PLoS Biol, 4, e193.  
15890913 A.Uchiyama, and B.A.Fane (2005).
Identification of an interacting coat-external scaffolding protein domain required for both the initiation of phiX174 procapsid morphogenesis and the completion of DNA packaging.
  J Virol, 79, 6751-6756.  
15687276 H.A.Wichman, J.Millstein, and J.J.Bull (2005).
Adaptive molecular evolution for 13,000 phage generations: a possible arms race.
  Genetics, 170, 19-31.  
15516569 I.N.Clarke, L.T.Cutcliffe, J.S.Everson, S.A.Garner, P.R.Lambden, P.J.Pead, M.A.Pickett, K.L.Brentlinger, and B.A.Fane (2004).
Chlamydiaphage Chp2, a skeleton in the phiX174 closet: scaffolding protein and procapsid identification.
  J Bacteriol, 186, 7571-7574.  
15383287 M.C.Morais, M.Fisher, S.Kanamaru, L.Przybyla, J.Burgner, B.A.Fane, and M.G.Rossmann (2004).
Conformational switching by the scaffolding protein D directs the assembly of bacteriophage phiX174.
  Mol Cell, 15, 991-997.
PDB code: 1tx9
11807069 K.L.Brentlinger, S.Hafenstein, C.R.Novak, B.A.Fane, R.Borgon, R.McKenna, and M.Agbandje-McKenna (2002).
Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus.
  J Bacteriol, 184, 1089-1094.  
11991963 S.Hafenstein, and B.A.Fane (2002).
phi X174 genome-capsid interactions influence the biophysical properties of the virion: evidence for a scaffolding-like function for the genome during the final stages of morphogenesis.
  J Virol, 76, 5350-5356.  
11000202 A.D.Burch, and B.A.Fane (2000).
Foreign and chimeric external scaffolding proteins as inhibitors of Microviridae morphogenesis.
  J Virol, 74, 9347-9352.  
10729119 B.L.Liu, J.S.Everson, B.Fane, P.Giannikopoulou, E.Vretou, P.R.Lambden, and I.N.Clarke (2000).
Molecular characterization of a bacteriophage (Chp2) from Chlamydia psittaci.
  J Virol, 74, 3464-3469.  
10997898 T.Dokland (2000).
Freedom and restraint: themes in virus capsid assembly.
  Structure, 8, R157-R162.  
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.

 

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