1XOK

crystal structure of alfalfa mosaic virus RNA 3'UTR in complex with coat protein N terminal peptide

• PDB DOI: https://doi.org/10.2210/pdb1XOK/pdb
• NAKB: 1XOK

• Classification: Viral protein/RNA
• Organism(s): Alfalfa mosaic virus (strain YSMV)
• Mutation(s): No 


• Deposited: 2004-10-06 Released: 2005-01-04 
• Deposition Author(s): Guogas, L.M., Filman, D.J., Hogle, J.M., Gehrke, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication.

Guogas, L.M., Filman, D.J., Hogle, J.M., Gehrke, L.

(2004) Science 306: 2108-2111

• PubMed: 15604410 
• DOI: https://doi.org/10.1126/science.1103399
• Primary Citation of Related Structures:  
  1XOK


• PubMed Abstract: 
  

  Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.

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Organizational Affiliation: 

Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.06 kDa 
• Atom Count: 1,017 
• Modelled Residue Count: 69 
• Deposited Residue Count: 91 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	C, D	26	N/A	Mutation(s): 0
UniProt
Find proteins for P24264 (Alfalfa mosaic virus (strain YSMV)) Explore P24264  Go to UniProtKB:  P24264

Entity ID: 1
Molecule	Chains	Length	Organism	Image
alfalfa mosaic virus RNA 3' UTR	A	30	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
alfalfa mosaic virus RNA 3' UTR	B	9	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	E [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.1	α = 90
b = 123	β = 90
c = 53.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-04 
Deposition Author(s): Guogas, L.M., Filman, D.J., Hogle, J.M., Gehrke, L.

Revision History  

• Version 1.0: 2005-01-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations