1HX6

P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution.

Benson, S.D., Bamford, J.K., Bamford, D.H., Burnett, R.M.

(2002) Acta Crystallogr D Biol Crystallogr 58: 39-59

  • DOI: 10.1107/s0907444901017279
  • Primary Citation of Related Structures:  
    1HQN, 1HX6

  • PubMed Abstract: 

    • P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now been extended to 1.65 A resolution (R(work) = 19.0% and R(free) = 20 ...

    P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now been extended to 1.65 A resolution (R(work) = 19.0% and R(free) = 20.8%). The new high-resolution model shows that P3 forms crystals through hydrophobic patches solvated by 2-methyl-2,4-pentanediol molecules. It reveals details of how the molecule's high stability may be achieved through ordered solvent in addition to intra- and intersubunit interactions. Of particular importance is a 'puddle' at the top of the molecule containing a four-layer deep hydration shell that cross-links a complex structural feature formed by 'trimerization loops'. These loops also link subunits by extending over a neighbor to reach the third subunit in the trimer. As each subunit has two eight-stranded viral jelly rolls, the trimer has a pseudo-hexagonal shape to allow close packing in its 240 hexavalent capsid positions. Flexible regions in P3 facilitate these interactions within the capsid and with the underlying membrane. A selenometh-ionine P3 derivative, with which the structure was solved, has been refined to 2.2 A resolution (R(work) = 20.1% and R(free) = 22.8%). The derivatized molecule is essentially unchanged, although synchrotron radiation has the curious effect of causing it to rotate about its threefold axis. P3 is a second example of a trimeric 'double-barrel' protein that forms a stable building block with optimal shape for constructing a large icosahedral viral capsid. A major difference is that hexon has long variable loops that distinguish different adenovirus species. The short loops in P3 and the severe constraints of its various interactions explain why the PRD1 family has highly conserved coat proteins.

    Related Citations: 
    • Viral Evolution Revealed by Bacteriophage PRD1 and Human Adenovirus Coat Protein Structures
      Benson, S.D., Bamford, J.K., Bamford, D.H., Burnett, R.M.
      (1999) Cell 98: 825
    • Crystallization of the Major Coat Protein of PRD1, a Bacteriophage with an Internal Membrane
      Stewart, P.L., Ghosh, S., Bamford, D.H., Burnett, R.M.
      (1993) J Mol Biol 230: 349
    • Capsomer Proteins of Bacteriophage PRD1, a Bacterial Virus with a Membrane
      Bamford, J.K., Bamford, D.H.
      (1990) Virology 177: 445
    • Type-specific Epitope Locations Revealed by X-ray Crystallographic Study of Adenovirus Type 5 Hexon
      Rux, J.J., Burnett, R.M.
      (2000) Mol Ther 1: 18
    Organizational Affiliation: 

    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR CAPSID PROTEINA, B, C394Enterobacteria phage PRD1Mutation(s): 0 
Gene Names: III
UniProt
Find proteins for P22535 (Enterobacteria phage PRD1)
Explore P22535 
Go to UniProtKB:  P22535
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22535
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
H [auth A],
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
Y [auth C],
Z [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
N [auth B],
O [auth B],
E [auth A],
F [auth A],
G [auth A],
N [auth B],
O [auth B],
P [auth B],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.96α = 90
b = 121.3β = 90
c = 126.39γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance