Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 19.49 kDa 
• Atom Count: 1279 
• Modelled Residue Count: 115 
• Deposited Residue Count: 134 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3VYX

Structural insights into RISC assembly facilitated by dsRNA binding domains of human RNA helicase (DHX9)

• DOI: 10.2210/pdb3VYX/pdb
• NDB: NA2070

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


• Deposited: 2012-10-05 Released: 2013-02-13 
• Deposition Author(s): Yuan, Y.A., Fu, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.263 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)

Fu, Q., Yuan, Y.A.

(2013) Nucleic Acids Res 

• PubMed: 23361462 
• DOI: 10.1093/nar/gkt042
• Primary Citation of Related Structures:  
  3VYX, 3VYY


• PubMed Abstract: 
  

Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.

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Organizational Affiliation: 

Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase A	A	114	Homo sapiens	Mutation(s): 0  Gene Names: DHX9, DDX9, LKP, NDH2 EC: 3.6.4.13
Find proteins for Q08211 (Homo sapiens) Explore Q08211  Go to UniProtKB:  Q08211
NIH Common Fund Data Resources
PHAROS:  Q08211 GTEx:  ENSG00000135829

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')	B, C	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.263 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.198	α = 90
b = 63.198	β = 90
c = 107.617	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-05 
• Released Date: 2013-02-13 
Deposition Author(s): Yuan, Y.A., Fu, Q.

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release