1M1C | pdb_00001m1c

Structure of the L-A virus

• PDB DOI: https://doi.org/10.2210/pdb1M1C/pdb

• Classification: VIRUS
• Organism(s): Saccharomyces cerevisiae virus L-A
• Mutation(s): No 


• Deposited: 2002-06-18 Released: 2002-10-02 
• Deposition Author(s): Naitow, H., Tang, J., Canady, M., Wickner, R.B., Johnson, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.268 (Depositor), 0.389 (DCC) 
• R-Value Work: 
  0.266 (Depositor), 0.389 (DCC) 

Literature

L-A virus at 3.4 A resolution reveals particle architecture and mRNA decapping mechanism.

Naitow, H., Tang, J., Canady, M., Wickner, R.B., Johnson, J.E.

(2002) Nat Struct Biol 9: 725-728

• PubMed: 12244300 
• DOI: https://doi.org/10.1038/nsb844
• Primary Citation Related Structures: 
  1M1C


• PubMed Abstract: 
  

  The structure of the yeast L-A virus was determined by X-ray crystallography at 3.4 A resolution. The L-A dsRNA virus is 400 A in diameter and contains a single protein shell of 60 asymmetric dimers of the coat protein, a feature common among the inner protein shells of dsRNA viruses and probably related to their unique mode of transcription and replication. The two identical subunits in each dimer are in non-equivalent environments and show substantially different conformations in specific surface regions. The L-A virus decaps cellular mRNA to efficiently translate its own uncapped mRNA. Our structure reveals a trench at the active site of the decapping reaction and suggests a role for nearby residues in the reaction.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 120-mer - A120 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 152.14 kDa 
• Atom Count: 10,302 
• Modeled Residue Count: 1,302 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major coat protein	A, B	680	Saccharomyces cerevisiae virus L-A	Mutation(s): 0
UniProt
Find proteins for P32503 (Saccharomyces cerevisiae virus L-A) Explore P32503  Go to UniProtKB:  P32503

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.268 (Depositor), 0.389 (DCC) 
• R-Value Work:  0.266 (Depositor), 0.389 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 407	α = 90
b = 403.2	β = 90.46
c = 572	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-02 
Deposition Author(s): Naitow, H., Tang, J., Canady, M., Wickner, R.B., Johnson, J.E.

Revision History  

• Version 1.0: 2002-10-02
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations