PDBsum entry 1vri

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Virus/viral protein PDB id
Protein chains
(+ 54 more) 309 a.a.
Theoretical model
PDB id:
Name: Virus/viral protein
Title: Bacteriophage phi-29 connector array. This file is one of three representing the entire carpet. This file, 1vri, includes the upper 5 monomers the other two files, 1ywe and 1vrj, contain the lower 5 and right 3 monomers respectively.
Structure: Upper collar protein. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, 1, 2, 3, 4, 5, 6, 7, 8. Synonym: connector protein, late protein gp10
Source: Bacteriophage phi-29. Virus
Authors: Y.Y.Guo,F.Blocker,F.Xiao,P.Guo
Key ref: Y.Y.Guo et al. (2005). Construction and 3-D computer modeling of connector arrays with tetragonal to decagonal transition induced by pRNA of phi29 DNA-packaging motor. J Nanosci Nanotechnol, 5, 856-863. PubMed id: 16060143
11-Apr-05     Release date:   20-Sep-05    
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Protein chains
Pfam   ArchSchema ?
P04332  (VG10_BPPH2) -  Upper collar protein
309 a.a.
309 a.a.
Key:    PfamA domain  Secondary structure


J Nanosci Nanotechnol 5:856-863 (2005)
PubMed id: 16060143  
Construction and 3-D computer modeling of connector arrays with tetragonal to decagonal transition induced by pRNA of phi29 DNA-packaging motor.
Y.Y.Guo, F.Blocker, F.Xiao, P.Guo.
The bottom-up assembly of patterned arrays is an exciting and important area in current nanotechnology. Arrays can be engineered to serve as components in chips for a virtually inexhaustible list of applications ranging from disease diagnosis to ultrahigh-density data storage. In attempting to achieve this goal, a number of methods to facilitate array design and production have been developed. Cloning and expression of the gene coding for the connector of the bacterial virus phi29 DNA-packaging motor, overproduction of the gene products, and the in vitro construction of large-scale carpet-like arrays composed of connector are described in this report. The stability of the arrays under various conditions, including varied pH, temperature and ionic strength, was tested. The addition of packaging RNA (pRNA) into the array caused a dramatic shift in array structure, and resulted in the conversion of tetragonal arrays into larger decagonal structures comprised of both protein and RNA. RNase digestion confirmed that the conformational shift was caused by pRNA, and that RNA was present in the decagons. As has been demonstrated in biomotors, conformational shift of motor components can generate force for motor motion. The conformational shift reported here can be utilized as a potential force-generating mechanism for the construction of nanomachines. Three-dimensional computer models of the constructed arrays were also produced using a variety of connector building blocks with or without the N- or C-terminal sequence, which is absent from the current published crystal structures. Both the connector array and the decagon are ideal candidates to be used as templates to build patterned suprastructures in nanotechnology.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20509670 F.Xiao, B.Demeler, and P.Guo (2010).
Assembly mechanism of the sixty-subunit nanoparticles via interaction of RNA with the reengineered protein connector of phi29 DNA-packaging motor.
  ACS Nano, 4, 3293-3301.  
20230868 P.Guo, O.Coban, N.M.Snead, J.Trebley, S.Hoeprich, S.Guo, and Y.Shu (2010).
Engineering RNA for targeted siRNA delivery and medical application.
  Adv Drug Deliv Rev, 62, 650-666.  
20523933 P.Jing, F.Haque, A.P.Vonderheide, C.Montemagno, and P.Guo (2010).
Robust properties of membrane-embedded connector channel of bacterial virus phi29 DNA packaging motor.
  Mol Biosyst, 6, 1844-1852.  
19893523 D.Wendell, P.Jing, J.Geng, V.Subramaniam, T.J.Lee, C.Montemagno, and P.Guo (2009).
Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores.
  Nat Nanotechnol, 4, 765-772.  
19206255 F.Xiao, J.Sun, O.Coban, P.Schoen, J.C.Wang, R.H.Cheng, and P.Guo (2009).
Fabrication of massive sheets of single layer patterned arrays using lipid directed reengineered phi29 motor dodecamer.
  ACS Nano, 3, 100-107.  
19634910 F.Xiao, Y.Cai, J.C.Wang, D.Green, R.H.Cheng, B.Demeler, and P.Guo (2009).
Adjustable ellipsoid nanoparticles assembled from re-engineered connectors of the bacteriophage phi29 DNA packaging motor.
  ACS Nano, 3, 2163-2170.  
19495981 T.J.Lee, C.Schwartz, and P.Guo (2009).
Construction of bacteriophage phi29 DNA packaging motor and its applications in nanotechnology and therapy.
  Ann Biomed Eng, 37, 2064-2081.  
15886394 F.Xiao, W.D.Moll, S.Guo, and P.Guo (2005).
Binding of pRNA to the N-terminal 14 amino acids of connector protein of bacteriophage phi29.
  Nucleic Acids Res, 33, 2640-2649.  
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