1R9F | pdb_00001r9f

Crystal structure of p19 complexed with 19-bp small interfering RNA

• PDB DOI: https://doi.org/10.2210/pdb1R9F/pdb
• NAKB: 1R9F

• Classification: Viral protein/RNA
• Organism(s): Tomato bushy stunt virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-10-28 Released: 2004-01-27 
• Deposition Author(s): Ye, K., Malinina, L., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Recognition of small interfering RNA by a viral suppressor of RNA

Ye, K., Malinina, L., Patel, D.J.

(2003) Nature 426: 874-878

• PubMed: 14661029 
• DOI: https://doi.org/10.1038/nature02213
• Primary Citation Related Structures: 
  1R9F


• PubMed Abstract: 
  

  RNA silencing (also known as RNA interference) is a conserved biological response to double-stranded RNA that regulates gene expression, and has evolved in plants as a defence against viruses. The response is mediated by small interfering RNAs (siRNAs), which guide the sequence-specific degradation of cognate messenger RNAs. As a counter-defence, many viruses encode proteins that specifically inhibit the silencing machinery. The p19 protein from the tombusvirus is such a viral suppressor of RNA silencing and has been shown to bind specifically to siRNA. Here, we report the 1.85-A crystal structure of p19 bound to a 21-nucleotide siRNA, where the 19-base-pair RNA duplex is cradled within the concave face of a continuous eight-stranded beta-sheet, formed across the p19 homodimer interface. Direct and water-mediated intermolecular contacts are restricted to the backbone phosphates and sugar 2'-OH groups, consistent with sequence-independent p19-siRNA recognition. Two alpha-helical 'reading heads' project from opposite ends of the p19 homodimer and position pairs of tryptophans for stacking over the terminal base pairs, thereby measuring and bracketing both ends of the siRNA duplex. Our structure provides an illustration of siRNA sequestering by a viral protein.

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Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.3 kDa 
• Atom Count: 1,862 
• Modeled Residue Count: 161 
• Deposited Residue Count: 178 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Core protein P19	C [auth A]	136	Tomato bushy stunt virus	Mutation(s): 3  Gene Names: p19
UniProt
Find proteins for P11690 (Tomato bushy stunt virus (strain Cherry)) Explore P11690  Go to UniProtKB:  P11690

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3'	A [auth B]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'	B [auth C]	21	N/A

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	C [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.230 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.249	α = 90
b = 91.249	β = 90
c = 148.63	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-27 
Deposition Author(s): Ye, K., Malinina, L., Patel, D.J.

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary