6M6S | pdb_00006m6s

Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain with 5'-ppp 12-mer dsRNA

• PDB DOI: https://doi.org/10.2210/pdb6M6S/pdb
• NAKB: 6M6S

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Caenorhabditis elegans, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-16 Released: 2021-03-17 
• Deposition Author(s): Li, K., Zheng, J., Wirawan, M., Xiong, Z., Fedorova, O., Griffin, P., Plyle, A., Luo, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3).

Li, K., Zheng, J., Wirawan, M., Trinh, N.M., Fedorova, O., Griffin, P.R., Pyle, A.M., Luo, D.

(2021) Nucleic Acids Res 49: 9978-9991

• PubMed: 34403472 
• DOI: https://doi.org/10.1093/nar/gkab712
• Primary Citation Related Structures: 
  6M6Q, 6M6R, 6M6S


• PubMed Abstract: 
  

  DRH-3 is critically involved in germline development and RNA interference (RNAi) facilitated chromosome segregation via the 22G-siRNA pathway in Caenorhabditis elegans. DRH-3 has similar domain architecture to RIG-I-like receptors (RLRs) and belongs to the RIG-I-like RNA helicase family. The molecular understanding of DRH-3 and its function in endogenous RNAi pathways remains elusive. In this study, we solved the crystal structures of the DRH-3 N-terminal domain (NTD) and the C-terminal domains (CTDs) in complex with 5'-triphosphorylated RNAs. The NTD of DRH-3 adopts a distinct fold of tandem caspase activation and recruitment domains (CARDs) structurally similar to the CARDs of RIG-I and MDA5, suggesting a signaling function in the endogenous RNAi biogenesis. The CTD preferentially recognizes 5'-triphosphorylated double-stranded RNAs bearing the typical features of secondary siRNA transcripts. The full-length DRH-3 displays unique structural dynamics upon binding to RNA duplexes that differ from RIG-I or MDA5. These features of DRH-3 showcase the evolutionary divergence of the Dicer and RLR family of helicases.

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Organizational Affiliation: 
• Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.
NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore.
The Scripps Research Institute, Jupiter, FL 33458, USA.
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.86 kDa 
• Atom Count: 3,644 
• Modeled Residue Count: 346 
• Deposited Residue Count: 364 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dicer Related Helicase	A, B	170	Caenorhabditis elegans	Mutation(s): 0  Gene Names: drh-3, CELE_D2005.5, D2005.5
UniProt
Find proteins for Q93413 (Caenorhabditis elegans) Explore Q93413  Go to UniProtKB:  Q93413

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')	C, D	12	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.775	α = 90
b = 93.09	β = 90
c = 133.823	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Li, K., Zheng, J., Wirawan, M., Xiong, Z., Fedorova, O., Griffin, P., Plyle, A., Luo, D.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2022-08-10
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description