Crystal structure of DHX8 helicase domain bound to ADP at 2.6 angstrom

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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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 476: 2521-2543

  • DOI: https://doi.org/10.1042/BCJ20190383
  • Primary Citation of Related Structures:  
    6HYS, 6HYT, 6HYU

  • 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 characterisation 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 the 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 the 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

    Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8
A, B, C, D
673Homo sapiensMutation(s): 0 
Gene Names: DHX8DDX8
UniProt & NIH Common Fund Data Resources
Find proteins for Q14562 (Homo sapiens)
Explore Q14562 
Go to UniProtKB:  Q14562
PHAROS:  Q14562
GTEx:  ENSG00000067596 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14562
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

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DA [auth C],
E [auth A],
PA [auth D],
R [auth B]
C10 H15 N5 O10 P2
Query on DMS

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AA [auth B]
BA [auth B]
CA [auth B]
G [auth A]
GA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
G [auth A],
GA [auth C],
HA [auth C],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
Q [auth A],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
ZA [auth D]
C2 H6 O S
Query on EDO

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FA [auth C]
H [auth A]
I [auth A]
RA [auth D]
SA [auth D]
FA [auth C],
H [auth A],
I [auth A],
RA [auth D],
SA [auth D],
W [auth B]
C2 H6 O2
Query on ACT

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AB [auth D],
L [auth A],
Z [auth B]
C2 H3 O2
Query on MG

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EA [auth C],
F [auth A],
QA [auth D],
S [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.96α = 90
b = 167.94β = 92.71
c = 137.11γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description