4JNX | pdb_00004jnx

Crystal structure of RNA silencing suppressor p19 complexed with double-helical RNA 20mer pG(CUG)6C

• PDB DOI: https://doi.org/10.2210/pdb4JNX/pdb
• NAKB: 4JNX

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


• Deposited: 2013-03-16 Released: 2014-03-19 
• Deposition Author(s): Katorcha, E., Popov, A.N., Malinina, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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: 42.15 kDa 
• Atom Count: 3,897 
• Modeled Residue Count: 288 
• Deposited Residue Count: 294 
• 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, B [auth D]	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*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'	C [auth B], D [auth G]	20	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth D], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	I [auth D], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.917	α = 90
b = 89.917	β = 90
c = 148.353	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: 2014-03-19 
Deposition Author(s): Katorcha, E., Popov, A.N., Malinina, L.

Revision History  

• Version 1.0: 2014-03-19
  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