4ANG | pdb_00004ang

Small RNA phage PRR1 in complex with an RNA operator fragment

• PDB DOI: https://doi.org/10.2210/pdb4ANG/pdb
• NAKB: 4ANG

• Classification: VIRUS
• Organism(s): Pseudomonas phage PRR1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-16 Released: 2013-02-27 
• Deposition Author(s): Persson, M., Tars, K., Liljas, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.313 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.308 (Depositor), 0.291 (DCC) 
• R-Value Observed: 
  0.308 (Depositor) 

Starting Model: experimental

Literature

Prr1 Coat Protein Binding to its RNA Translational Operator

Persson, M., Tars, K., Liljas, L.

(2013) Acta Crystallogr D Biol Crystallogr 69: 367

• PubMed: 23519411 
• DOI: https://doi.org/10.1107/S0907444912047464
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

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

Macromolecule Content 

• Total Structure Weight: 56.56 kDa 
• Atom Count: 3,863 
• Modeled Residue Count: 420 
• Deposited Residue Count: 433 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAT PROTEIN	A, B, C	131	Pseudomonas phage PRR1	Mutation(s): 0
UniProt
Find proteins for P03616 (Pseudomonas phage PRR1) Explore P03616  Go to UniProtKB:  P03616

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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]	20	Pseudomonas phage PRR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.313 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.308 (Depositor), 0.291 (DCC) 
• R-Value Observed: 0.308 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 281.3	α = 93.23
b = 285.4	β = 90.03
c = 472.9	γ = 119.45

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Persson, M., Tars, K., Liljas, L.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-04-03
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description