Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 39.24 kDa 
• Atom Count: 2,829 
• Modelled Residue Count: 282 
• Deposited Residue Count: 284 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 3OG8

Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA

• PDB DOI:  https://doi.org/10.2210/pdb3OG8/pdb
• NDB: NA0659

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-16 Released: 2010-11-03 
• Deposition Author(s): Li, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.278 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5' triphosphate.

Lu, C., Ranjith-Kumar, C.T., Hao, L., Kao, C.C., Li, P.

(2011) Nucleic Acids Res 39: 1565-1575

• PubMed: 20961956 
• DOI: https://doi.org/10.1093/nar/gkq974
• Primary Citation of Related Structures:  
  3OG8


• PubMed Abstract: 
  

RIG-I recognizes molecular patterns in viral RNA to regulate the induction of type I interferons. The C-terminal domain (CTD) of RIG-I exhibits high affinity for 5' triphosphate (ppp) dsRNA as well as blunt-ended dsRNA. Structures of RIG-I CTD bound to 5'-ppp dsRNA showed that RIG-I recognizes the termini of dsRNA and interacts with the ppp through electrostatic interactions. However, the structural basis for the recognition of non-phosphorylated dsRNA by RIG-I is not fully understood. Here, we show that RIG-I CTD binds blunt-ended dsRNA in a different orientation compared to 5' ppp dsRNA and interacts with both strands of the dsRNA. Overlapping sets of residues are involved in the recognition of blunt-ended dsRNA and 5' ppp dsRNA. Mutations at the RNA-binding surface affect RNA binding and signaling by RIG-I. These results provide the mechanistic basis for how RIG-I recognizes different RNA ligands.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX58	A, B	128	Homo sapiens	Mutation(s): 1  Gene Names: DDX58 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O95786 (Homo sapiens) Explore O95786  Go to UniProtKB:  O95786
PHAROS:  O95786

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')	C, D	14	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.278 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.99	α = 90
b = 70.3	β = 90
c = 125.54	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Li, P.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance