6Q6R

Recognition of different base tetrads by RHAU: X-ray crystal structure of G4 recognition motif bound to the 3-end tetrad of a DNA G-quadruplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3'-end tetrad of a DNA G-quadruplex.

Heddi, B.Cheong, V.V.Schmitt, E.Mechulam, Y.Phan, A.T.

(2020) J Struct Biol 209: 107399-107399

  • DOI: 10.1016/j.jsb.2019.10.001
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • G-quadruplexes (G4) are secondary structures of nucleic acids that can form in cells and have diverse biological functions. Several biologically important proteins interact with G-quadruplexes, of which RHAU (or DHX36) - a helicase from the DEAH-box ...

    G-quadruplexes (G4) are secondary structures of nucleic acids that can form in cells and have diverse biological functions. Several biologically important proteins interact with G-quadruplexes, of which RHAU (or DHX36) - a helicase from the DEAH-box superfamily, was shown to bind and unwind G-quadruplexes efficiently. We report a X-ray co-crystal structure at 1.5 Å resolution of an N-terminal fragment of RHAU bound to an exposed tetrad of a parallel-stranded G-quadruplex. The RHAU peptide folds into an L-shaped α-helix, and binds to a G-quadruplex through π-stacking and electrostatic interactions. X-ray crystal structure of our complex identified key amino acid residues important for G-quadruplex-peptide binding interaction at the 3'-end G•G•G•G tetrad. Together with previous solution and crystal structures of RHAU bound to the 5'-end G•G•G•G and G•G•A•T tetrads, our crystal structure highlights the occurrence of a robust G-quadruplex recognition motif within RHAU that can adapt to different accessible tetrads.


    Organizational Affiliation

    School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore. Electronic address: phantuan@ntu.edu.sg.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent DNA/RNA helicase DHX36
E, F, G, H
29Homo sapiensMutation(s): 0 
Gene Names: DHX36DDX36KIAA1488MLEL1RHAU
EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
Find proteins for Q9H2U1 (Homo sapiens)
Go to UniProtKB:  Q9H2U1
NIH Common Fund Data Resources
PHAROS  Q9H2U1
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
Parallel stranded DNA G-quadruplexA, B,C,D16unidentified
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.39α = 90
b = 42.25β = 99.3
c = 61.404γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)SingaporeNRF-NRFI2017-09
Ministry of Education (Singapore)SingaporeMOE2012-T3-1-001

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2020-01-22
    Changes: Database references