6JJH

Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths.

Zhang, Y.El Omari, K.Duman, R.Liu, S.Haider, S.Wagner, A.Parkinson, G.N.Wei, D.

(2020) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkaa439
  • Primary Citation of Related Structures:  
    6JJF, 6JJI, 6JJH, 6TQI

  • PubMed Abstract: 
  • Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to na ...

    Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.


    Organizational Affiliation

    College of Science, Huazhong Agricultural University, Wuhan 430070, China.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')B14Pseudorabies virus Ea
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    POH
    Query on POH

    Download CCD File 
    B
    (1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin
    C44 H38 N8
    ABCGFHPGHXSVKI-LWQDQPMZSA-O
     Ligand Interaction
    K
    Query on K

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.74 Å
    • R-Value Free: 0.291 
    • R-Value Work: 0.239 
    • R-Value Observed: 0.242 
    • Space Group: P 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 29.856α = 90
    b = 23.647β = 107.59
    c = 31.052γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    PDB_EXTRACTdata extraction
    XDSdata reduction
    XSCALEdata scaling
    Aimlessdata scaling
    HKL2Mapphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of China (NSFC)China31672558

    Revision History 

    • Version 1.0: 2020-02-26
      Type: Initial release
    • Version 1.1: 2020-09-09
      Changes: Database references, Derived calculations