6HYU

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

• PDB DOI:  https://doi.org/10.2210/pdb6HYU/pdb
• NAKB: 6HYU

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-10-22 Released: 2019-08-28 
• Deposition Author(s): Felisberto-Rodrigues, C., Thomas, J.C., McAndrew, P.C., Le Bihan, Y.V., Burke, R., Workman, P., van Montfort, R.L.M.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 0.289 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

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 476: 2521-2543

• PubMed: 31409651 
• 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.

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Organizational Affiliation: 

Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, U.K.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 156.58 kDa 
• Atom Count: 8,921 
• Modelled Residue Count: 1,210 
• Deposited Residue Count: 1,355 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DHX8	A, C	673	Homo sapiens	Mutation(s): 0  Gene Names: DHX8, DDX8 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q14562 (Homo sapiens) Explore Q14562  Go to UniProtKB:  Q14562
PHAROS:  Q14562

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')	B	6	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*A*AP*A)-3')	D	3	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 0.289 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.104	α = 90
b = 138.601	β = 90
c = 169.143	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Felisberto-Rodrigues, C., Thomas, J.C., McAndrew, P.C., Le Bihan, Y.V., Burke, R., Workman, P., van Montfort, R.L.M.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C309/A11566
Cancer Research UK	United Kingdom	C2739/A22897

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references