2W0C

X-ray structure of the entire lipid-containing bacteriophage PM2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7 Å
  • R-Value Work: 0.419 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights Into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage Pm2

Abrescia, N.G.A.Grimes, J.M.Kivela, H.M.Assenberg, R.Sutton, G.C.Butcher, S.J.Bamford, J.K.H.Bamford, D.H.Stuart, D.I.

(2008) Mol.Cell 31: 749

  • DOI: 10.1016/j.molcel.2008.06.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent, primarily structural observations indicate that related viruses, harboring no sequence similarity, infect hosts of different domains of life. One such clade of viruses, defined by common capsid architecture and coat protein fold, is the so-ca ...

    Recent, primarily structural observations indicate that related viruses, harboring no sequence similarity, infect hosts of different domains of life. One such clade of viruses, defined by common capsid architecture and coat protein fold, is the so-called PRD1-adenovirus lineage. Here we report the structure of the marine lipid-containing bacteriophage PM2 determined by crystallographic analyses of the entire approximately 45 MDa virion and of the outer coat proteins P1 and P2, revealing PM2 to be a primeval member of the PRD1-adenovirus lineage with an icosahedral shell and canonical double beta barrel major coat protein. The view of the lipid bilayer, richly decorated with membrane proteins, constitutes a rare visualization of an in vivo membrane. The viral membrane proteins P3 and P6 are organized into a lattice, suggesting a possible assembly pathway to produce the mature virus.


    Related Citations: 
    • Selenomethionine Labeling of Large Biological Macromolecular Complexes: Probing the Structure of Marine Bacterial Virus Pm2.
      Kivela, H.M.,Abrescia, N.G.A.,Bamford, J.K.H.,Grimes, J.M.,Stuart, D.I.,Bamford, D.H.
      (2008) J.Struct.Biol. 161: 204
    • Preliminary Crystallographic Analysis of the Major Capsid Protein P2 of the Lipid-Containing Bacteriophage Pm2.
      Abrescia, N.G.A.,Kivela, H.M.,Grimes, J.M.,Bamford, J.K.H.,Bamford, D.H.,Stuart, D.I.
      (2005) Acta Crystallogr.,Sect.F 61: 762


    Organizational Affiliation

    Division of Structural Biology and the Oxford Protein Production Facility, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR CAPSID PROTEIN P2
A, B, C, D, E, F, G, H, I, J
269Pseudoalteromonas phage PM2Mutation(s): 0 
Gene Names: II
Find proteins for P15794 (Pseudoalteromonas phage PM2)
Go to UniProtKB:  P15794
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN 2
L
335Pseudoalteromonas phage PM2Mutation(s): 0 
Gene Names: I
Find proteins for Q9XJR3 (Pseudoalteromonas phage PM2)
Go to UniProtKB:  Q9XJR3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN P3
P, Q, R, S
104Pseudoalteromonas phage PM2Mutation(s): 0 
Gene Names: III
Find proteins for Q9XJR6 (Pseudoalteromonas phage PM2)
Go to UniProtKB:  Q9XJR6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN P6
T
127Pseudoalteromonas phage PM2Mutation(s): 0 
Gene Names: VI
Find proteins for Q9XJR1 (Pseudoalteromonas phage PM2)
Go to UniProtKB:  Q9XJR1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7 Å
  • R-Value Work: 0.419 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 946.900α = 90.00
b = 677.600β = 102.90
c = 1067.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Data collection