3ZD7 | pdb_00003zd7

Snapshot 3 of RIG-I scanning on RNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.288 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Defining the Functional Determinants for RNA Surveillance by Rig-I.

Kohlway, A.Luo, D.Rawling, D.C.Ding, S.C.Pyle, A.M.

(2013) EMBO Rep 14: 772

  • DOI: https://doi.org/10.1038/embor.2013.108
  • Primary Citation Related Structures: 
    3ZD6, 3ZD7

  • PubMed Abstract: 

    Retinoic acid-inducible gene-I (RIG-I) is an intracellular RNA sensor that activates the innate immune machinery in response to infection by RNA viruses. Here, we report the crystal structure of distinct conformations of a RIG-I:dsRNA complex, which shows that HEL2i-mediated scanning allows RIG-I to sense the length of RNA targets. To understand the implications of HEL2i scanning for catalytic activity and signalling by RIG-I, we examined its ATPase activity when stimulated by duplex RNAs of varying lengths and 5' composition. We identified a minimal RNA duplex that binds one RIG-I molecule, stimulates robust ATPase activity, and elicits a RIG-I-mediated interferon response in cells. Our results reveal that the minimal functional unit of the RIG-I:RNA complex is a monomer that binds at the terminus of a duplex RNA substrate. This behaviour is markedly different from the RIG-I paralog melanoma differentiation-associated gene 5 (MDA5), which forms cooperative filaments.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry.

Macromolecule Content 

  • Total Structure Weight: 86.64 kDa 
  • Atom Count: 5,369 
  • Modeled Residue Count: 643 
  • Deposited Residue Count: 716 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROBABLE ATP-DEPENDENT RNA HELICASE DDX58696Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000107201 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95786
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA DUPLEXB [auth C],
C [auth D]
10synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.288 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.252α = 90
b = 75.996β = 90
c = 207.279γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary