4ANG

Small RNA phage PRR1 in complex with an RNA operator fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.308 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Prr1 Coat Protein Binding to its RNA Translational Operator

Persson, M.Tars, K.Liljas, L.

(2013) Acta Crystallogr.,Sect.D 69: 367

  • DOI: 10.1107/S0907444912047464

  • PubMed Abstract: 
  • In small RNA bacteriophages, the genomic RNA binds to the coat proteins when the viral capsid assembles. This is achieved through sequence-specific interactions between a coat-protein dimer and an RNA stem-loop that includes the start codon for the r ...

    In small RNA bacteriophages, the genomic RNA binds to the coat proteins when the viral capsid assembles. This is achieved through sequence-specific interactions between a coat-protein dimer and an RNA stem-loop that includes the start codon for the replicase gene. The structure of virus-like particles of the small RNA phage PRR1 bound to an RNA segment corresponding to this stem-loop has been solved and the binding was compared with the related, and better investigated, phage MS2. The overall conformation of the RNA is found to be similar and the residues that are involved in RNA binding in PRR1 are the same as in MS2. The arrangement of the nucleotide bases in the loop of the stem-loop is different, leading to a difference in the stacking at the conserved Tyr86, which is equivalent to Tyr85 in MS2.


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, BMC, Husargatan 3, Box 596, S-751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN
A, B, C
131Pseudomonas phage PRR1Mutation(s): 0 
Find proteins for P03616 (Pseudomonas phage PRR1)
Go to UniProtKB:  P03616
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'R,S20Pseudomonas phage PRR1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.308 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 281.300α = 93.23
b = 285.400β = 90.03
c = 472.900γ = 119.45
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references