Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 37873.28 
• Atom Count: 2620 
• Residue Count: 270 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3LRN

Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp dsRNA

• DOI: 10.2210/pdb3LRN/pdb
• NDB: NA0444

• Classification: Hydrolase/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2010-02-11 Released: 2010-06-02 
• Deposition Author(s): Li, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.282 
• R-Value Work: 0.221 

Literature

The Structural Basis of 5' Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain.

Lu, C., Xu, H., Ranjith-Kumar, C.T., Brooks, M.T., Hou, T.Y., Hu, F., Herr, A.B., Strong, R.K., Kao, C.C., Li, P.

(2010) Structure 18: 1032-1043

• PubMed: 20637642 
• DOI: 10.1016/j.str.2010.05.007
• Primary Citation of Related Structures:  
  3LRR


• PubMed Abstract: 
  

RIG-I is a cytosolic sensor of viral RNA that plays crucial roles in the induction of type I interferons. The C-terminal domain (CTD) of RIG-I is responsible for the recognition of viral RNA with 5' triphosphate (ppp). However, the mechanism of viral RNA recognition by RIG-I is still not fully understood. Here, we show that RIG-I CTD binds 5' ppp dsRNA or ssRNA, as well as blunt-ended dsRNA, and exhibits the highest affinity for 5' ppp dsRNA. Crystal structures of RIG-I CTD bound to 5' ppp dsRNA with GC- and AU-rich sequences revealed that RIG-I recognizes the termini of the dsRNA and interacts with the 5' ppp through extensive electrostatic interactions. Mutagenesis and RNA-binding studies demonstrated that similar binding surfaces are involved in the recognition of different forms of RNA. Mutations of key residues at the RNA-binding surface affected RIG-I signaling in cells.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Probable ATP-dependent RNA helicase DDX58	A, B	121	Homo sapiens	Mutation(s): 1  Gene Names: DDX58
Find proteins for O95786 (Homo sapiens) Go to Gene View: DDX58 Go to UniProtKB:  O95786

Entity ID: 2
Molecule	Chains	Length	Organism
RNA (5'-R(*(GTP)P*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 & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GTP	C, D	NON-POLYMER	C10 H16 N5 O14 P3		G

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.282 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 41.490	α = 90.00
b = 96.330	β = 90.00
c = 103.400	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-11 
• Released Date: 2010-06-02 
• Deposition Author(s): Li, P.

Revision History 

• Version 1.0: 2010-06-02
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance