1CD3

PROCAPSID OF BACTERIOPHAGE PHIX174


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Work: 0.275 

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This is version 1.5 of the entry. See complete history


Literature

The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174.

Dokland, T.Bernal, R.A.Burch, A.Pletnev, S.Fane, B.A.Rossmann, M.G.

(1999) J Mol Biol 288: 595-608

  • DOI: https://doi.org/10.1006/jmbi.1999.2699
  • Primary Citation of Related Structures:  
    1CD3

  • PubMed 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.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907-1392, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SCAFFOLDING PROTEIN GPD)A [auth 1],
B [auth 2],
C [auth 3],
D [auth 4]
152Sinsheimervirus phiX174Mutation(s): 0 
UniProt
Find proteins for P69486 (Enterobacteria phage phiX174)
Explore P69486 
Go to UniProtKB:  P69486
Entity Groups  
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UniProt GroupP69486
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (CAPSID PROTEIN GPF)E [auth F]426Sinsheimervirus phiX174Mutation(s): 0 
UniProt
Find proteins for P03641 (Enterobacteria phage phiX174)
Explore P03641 
Go to UniProtKB:  P03641
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UniProt GroupP03641
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SPIKE PROTEIN GPG)F [auth G]175Sinsheimervirus phiX174Mutation(s): 0 
UniProt
Find proteins for P03643 (Enterobacteria phage phiX174)
Explore P03643 
Go to UniProtKB:  P03643
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UniProt GroupP03643
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SCAFFOLDING PROTEIN GPB)G [auth B]120Sinsheimervirus phiX174Mutation(s): 0 
UniProt
Find proteins for P03633 (Enterobacteria phage phiX174)
Explore P03633 
Go to UniProtKB:  P03633
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UniProt GroupP03633
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Work: 0.275 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 774α = 90
b = 774β = 90
c = 774γ = 90
Software Package:
Software NamePurpose
MGRmodel building
X-PLORrefinement
DENZOdata reduction
SnBphasing
MGRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-14
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.5: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations