Journal: Nature / Year: 2004 Title: Insights into assembly from structural analysis of bacteriophage PRD1. Authors: Nicola G A Abrescia / Joseph J B Cockburn / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / Sarah J Butcher / Stephen D Fuller / Carmen San Martín / Roger M Burnett / David I ...Authors: Nicola G A Abrescia / Joseph J B Cockburn / Jonathan M Grimes / Geoffrey C Sutton / Jonathan M Diprose / Sarah J Butcher / Stephen D Fuller / Carmen San Martín / Roger M Burnett / David I Stuart / Dennis H Bamford / Jaana K H Bamford / Abstract: The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 ...The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 and P31. Different structural proteins seem to have specialist roles in controlling virus assembly. The linearly extended P30 appears to nucleate the formation of the icosahedral facets (composed of trimers of the major capsid protein, P3) and acts as a molecular tape-measure, defining the size of the virus and cementing the facets together. Pentamers of P31 form the vertex base, interlocking with subunits of P3 and interacting with the membrane protein P16. The architectural similarities with adenovirus and one of the largest known virus particles PBCV-1 support the notion that the mechanism of assembly of PRD1 is scaleable and applies across the major viral lineage formed by these viruses.
History
Deposition
Oct 1, 2004
Deposition site: PDBE / Processing site: PDBE
Revision 1.0
Nov 11, 2004
Provider: repository / Type: Initial release
Revision 1.1
Apr 15, 2015
Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Version format compliance
SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.
A: MAJOR CAPSID PROTEIN (PROTEIN P3) B: MAJOR CAPSID PROTEIN (PROTEIN P3) C: MAJOR CAPSID PROTEIN (PROTEIN P3) D: MAJOR CAPSID PROTEIN (PROTEIN P3) E: MAJOR CAPSID PROTEIN (PROTEIN P3) F: MAJOR CAPSID PROTEIN (PROTEIN P3) G: MAJOR CAPSID PROTEIN (PROTEIN P3) H: MAJOR CAPSID PROTEIN (PROTEIN P3) I: MAJOR CAPSID PROTEIN (PROTEIN P3) J: MAJOR CAPSID PROTEIN (PROTEIN P3) K: MAJOR CAPSID PROTEIN (PROTEIN P3) L: MAJOR CAPSID PROTEIN (PROTEIN P3) M: PROTEIN P30 N: PROTEIN P31 P: PROTEIN P16
A: MAJOR CAPSID PROTEIN (PROTEIN P3) B: MAJOR CAPSID PROTEIN (PROTEIN P3) C: MAJOR CAPSID PROTEIN (PROTEIN P3) D: MAJOR CAPSID PROTEIN (PROTEIN P3) E: MAJOR CAPSID PROTEIN (PROTEIN P3) F: MAJOR CAPSID PROTEIN (PROTEIN P3) G: MAJOR CAPSID PROTEIN (PROTEIN P3) H: MAJOR CAPSID PROTEIN (PROTEIN P3) I: MAJOR CAPSID PROTEIN (PROTEIN P3) J: MAJOR CAPSID PROTEIN (PROTEIN P3) K: MAJOR CAPSID PROTEIN (PROTEIN P3) L: MAJOR CAPSID PROTEIN (PROTEIN P3) M: PROTEIN P30 N: PROTEIN P31 P: PROTEIN P16
A: MAJOR CAPSID PROTEIN (PROTEIN P3) B: MAJOR CAPSID PROTEIN (PROTEIN P3) C: MAJOR CAPSID PROTEIN (PROTEIN P3) D: MAJOR CAPSID PROTEIN (PROTEIN P3) E: MAJOR CAPSID PROTEIN (PROTEIN P3) F: MAJOR CAPSID PROTEIN (PROTEIN P3) G: MAJOR CAPSID PROTEIN (PROTEIN P3) H: MAJOR CAPSID PROTEIN (PROTEIN P3) I: MAJOR CAPSID PROTEIN (PROTEIN P3) J: MAJOR CAPSID PROTEIN (PROTEIN P3) K: MAJOR CAPSID PROTEIN (PROTEIN P3) L: MAJOR CAPSID PROTEIN (PROTEIN P3) M: PROTEIN P30 N: PROTEIN P31 P: PROTEIN P16
x 5
icosahedral pentamer
2.79 MDa, 75 polymers
Theoretical mass
Number of molelcules
Total (without water)
2,785,534
75
Polymers
2,785,534
75
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
4
4
A: MAJOR CAPSID PROTEIN (PROTEIN P3) B: MAJOR CAPSID PROTEIN (PROTEIN P3) C: MAJOR CAPSID PROTEIN (PROTEIN P3) D: MAJOR CAPSID PROTEIN (PROTEIN P3) E: MAJOR CAPSID PROTEIN (PROTEIN P3) F: MAJOR CAPSID PROTEIN (PROTEIN P3) G: MAJOR CAPSID PROTEIN (PROTEIN P3) H: MAJOR CAPSID PROTEIN (PROTEIN P3) I: MAJOR CAPSID PROTEIN (PROTEIN P3) J: MAJOR CAPSID PROTEIN (PROTEIN P3) K: MAJOR CAPSID PROTEIN (PROTEIN P3) L: MAJOR CAPSID PROTEIN (PROTEIN P3) M: PROTEIN P30 N: PROTEIN P31 P: PROTEIN P16
x 6
icosahedral 23 hexamer
3.34 MDa, 90 polymers
Theoretical mass
Number of molelcules
Total (without water)
3,342,641
90
Polymers
3,342,641
90
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
5
5
Idetical with deposited unit in distinct coordinate
icosahedral asymmetric unit, std point frame
Type
Name
Symmetry operation
Number
transform to point frame
1
6
A: MAJOR CAPSID PROTEIN (PROTEIN P3) B: MAJOR CAPSID PROTEIN (PROTEIN P3) C: MAJOR CAPSID PROTEIN (PROTEIN P3) D: MAJOR CAPSID PROTEIN (PROTEIN P3) E: MAJOR CAPSID PROTEIN (PROTEIN P3) F: MAJOR CAPSID PROTEIN (PROTEIN P3) G: MAJOR CAPSID PROTEIN (PROTEIN P3) H: MAJOR CAPSID PROTEIN (PROTEIN P3) I: MAJOR CAPSID PROTEIN (PROTEIN P3) J: MAJOR CAPSID PROTEIN (PROTEIN P3) K: MAJOR CAPSID PROTEIN (PROTEIN P3) L: MAJOR CAPSID PROTEIN (PROTEIN P3) M: PROTEIN P30 N: PROTEIN P31 P: PROTEIN P16
x 60
crystal asymmetric unit, crystal frame
33.4 MDa, 900 polymers
Theoretical mass
Number of molelcules
Total (without water)
33,426,409
900
Polymers
33,426,409
900
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
2
point symmetry operation
59
Unit cell
Length a, b, c (Å)
903.000, 920.600, 926.200
Angle α, β, γ (deg.)
90.00, 90.00, 90.00
Int Tables number
19
Space group name H-M
P212121
Symmetry
Point symmetry: (Schoenflies symbol: I (icosahedral))