6HYU

Crystal structure of DHX8 helicase bound to single stranded poly-adenine RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release.

Felisberto-Rodrigues, C.Thomas, J.C.McAndrew, C.Le Bihan, Y.V.Burke, R.Workman, P.van Montfort, R.L.M.

(2019) Biochem.J. --: --

  • DOI: 10.1042/BCJ20190383
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DHX8 is a crucial DEAH-box RNA helicase involved in splicing and required for the release of mature mRNA from the spliceosome. Here we report the biochemical characterization of full-length human DHX8 and the catalytically active helicase core DHX8Δ5 ...

    DHX8 is a crucial DEAH-box RNA helicase involved in splicing and required for the release of mature mRNA from the spliceosome. Here we report the biochemical characterization of full-length human DHX8 and the catalytically active helicase core DHX8Δ547, alongside crystal structures of DHX8Δ547 bound to ADP and a structure of DHX8Δ547 bound to poly(A) 6 single-strand RNA. Our results reveal that DHX8 has an in vitro binding preference for adenine-rich RNA and that RNA binding triggers release of ADP through significant conformational flexibility in the conserved DEAH-, P-loop and hook-turn motifs. We demonstrate the importance of R620 and both the hook-turn and hook-loop regions for DHX8 helicase activity, and propose that the hook-turn acts as a gatekeeper to regulate directional movement of the 3' end of RNA through the RNA binding channel. This study provides an in-depth understanding of the activity of DHX8 and contributes insights into the RNA unwinding mechanisms of the DEAH-box helicase family.


    Organizational Affiliation

    Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, United Kingdom.,The Insititute of Cancer Research, London, SM2 5NG, United Kingdom.,The Institute of Cancer Research, London, SM2 5NG, United Kingdom.,Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, United Kingdom rob.vanmontfort@icr.ac.uk.,Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Division of Cancer Therapeutics, London, SM2 5NG, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DHX8
A, C
673Homo sapiensMutation(s): 0 
Gene Names: DHX8 (DDX8)
EC: 3.6.4.13
Find proteins for Q14562 (Homo sapiens)
Go to Gene View: DHX8
Go to UniProtKB:  Q14562
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')B6synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*A*AP*A)-3')D3synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 66.104α = 90.00
b = 138.601β = 90.00
c = 169.143γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A11566
Cancer Research UKUnited KingdomC2739/A22897

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release