4ANG

Small RNA phage PRR1 in complex with an RNA operator fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.308 
  • R-Value Observed: 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 D Biol Crystallogr 69: 367

  • DOI: 10.1107/S0907444912047464
  • Primary Citation of Related Structures:  
    4ANG

  • 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 replicase gene ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COAT PROTEINA, B, C131Pseudomonas phage PRR1Mutation(s): 0 
UniProt
Find proteins for P03616 (Pseudomonas phage PRR1)
Explore P03616 
Go to UniProtKB:  P03616
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03616
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'D [auth R],
E [auth S]
20Pseudomonas phage PRR1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.308 
  • R-Value Observed: 0.308 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 281.3α = 93.23
b = 285.4β = 90.03
c = 472.9γ = 119.45
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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