4JGN

Crystal structure of RNA silencing suppressor p19 with 1nt-5'-overhanging double-helical RNA 20mer pUUG(CUG)5CU

• PDB DOI: https://doi.org/10.2210/pdb4JGN/pdb
• NAKB: 4JGN

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Tomato bushy stunt virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-01 Released: 2014-03-05 
• Deposition Author(s): Katorcha, E., Tamjar, J., Popov, A.N., Malinina, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Procrustean bed of RNA silencing suppression

Katorcha, E., Tamjar, J., Popov, A.N., Malinina, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 21.01 kDa 
• Atom Count: 1,575 
• Modelled Residue Count: 145 
• Deposited Residue Count: 147 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA silencing suppressor p19	A	127	Tomato bushy stunt virus	Mutation(s): 0  Gene Names: ORF4
UniProt
Find proteins for P69517 (Tomato bushy stunt virus (strain Ja9)) Explore P69517  Go to UniProtKB:  P69517

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(P*UP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'	B [auth E]	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.362	α = 90
b = 89.362	β = 90
c = 147.936	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Katorcha, E., Tamjar, J., Popov, A.N., Malinina, L.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description