2RMJ | pdb_00002rmj

Solution structure of RIG-I C-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb2RMJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-23 Released: 2008-03-25 
• Deposition Author(s): Takahasi, K., Yoneyama, M., Nihishori, T., Hirai, R., Narita, R., Gale Jr., M., Fujita, T., Inagaki, F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Nonself RNA-Sensing Mechanism of RIG-I Helicase and Activation of Antiviral Immune Responses

Takahasi, K., Yoneyama, M., Nishihori, T., Hirai, R., Kumeta, H., Narita, R., Gale Jr., M., Inagaki, F., Fujita, T.

(2008) Mol Cell 29: 428-440

• PubMed: 18242112 
• DOI: https://doi.org/10.1016/j.molcel.2007.11.028
• Primary Citation Related Structures: 
  2RMJ


• PubMed Abstract: 
  

  A DExD/H protein, RIG-I, is critical in innate antiviral responses by sensing viral RNA. Here we show that RIG-I recognizes two distinct viral RNA patterns: double-stranded (ds) and 5'ppp single-stranded (ss) RNA. The binding of RIG-I with dsRNA or 5'ppp ssRNA in the presence of ATP produces a common structure, as suggested by protease digestion. Further analyses demonstrated that the C-terminal domain of RIG-I (CTD) recognizes these RNA patterns and CTD coincides with the autorepression domain. Structural analysis of CTD by NMR spectroscopy in conjunction with mutagenesis revealed that the basic surface of CTD with a characteristic cleft interacts with RIG-I ligands. Our results suggest that the bipartite structure of CTD regulates RIG-I on encountering viral RNA patterns.

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Organizational Affiliation: 
• Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.66 kDa 
• Atom Count: 1,099 
• Modeled Residue Count: 134 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX58	A	134	Homo sapiens	Mutation(s): 0  Gene Names: DDX58 EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95786 (Homo sapiens) Explore O95786  Go to UniProtKB:  O95786
PHAROS:  O95786 GTEx:  ENSG00000107201

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Takahasi, K., Yoneyama, M., Nihishori, T., Hirai, R., Narita, R., Gale Jr., M., Fujita, T., Inagaki, F.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Database references, Derived calculations
• Version 1.3: 2024-05-29
  Changes: Data collection