9T99 | pdb_00009t99

Structure of C. elegans Dicer-related helicase 1 (DRH1) bound to blunt end 5'P-dsRNA

• PDB DOI: https://doi.org/10.2210/pdb9T99/pdb
• NAKB: 9T99

• Classification: RNA BINDING PROTEIN
• Organism(s): Caenorhabditis elegans, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-11-14 Released: 2025-11-26 
• Deposition Author(s): Cusack, S., Uchikawa, E.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structure of C. elegans Dicer-related helicase 1 (DRH1) bound to blunt end 5'P-dsRNA

Cusack, S., Uchikawa, E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.64 kDa 
• Atom Count: 6,470 
• Modeled Residue Count: 735 
• Deposited Residue Count: 763 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dicer-related helicase	A	728	Caenorhabditis elegans	Mutation(s): 1  Gene Names: drh-1, CELE_F15B10.2, F15B10.2
UniProt
Find proteins for G5EDI8 (Caenorhabditis elegans) Explore G5EDI8  Go to UniProtKB:  G5EDI8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*UP*AP*GP*UP*CP*UP*AP*CP*C)-3')	B [auth S]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')	C [auth X], D [auth Y]	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	F [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.354	α = 90
b = 134.354	β = 90
c = 221.301	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Cusack, S., Uchikawa, E.

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Funding Organization	Location	Grant Number
Other government	Germany	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2026-01-21
  Changes: Derived calculations