7C45

The crystal structure of Trypanosoma brucei RNase D complex with RNA U12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei.

Gao, Y.Liu, H.Zhang, C.Su, S.Chen, Y.Chen, X.Li, Y.Shao, Z.Zhang, Y.Shao, Q.Li, J.Huang, Z.Ma, J.Gan, J.

(2021) Nucleic Acids Res 49: 568-583

  • DOI: 10.1093/nar/gkaa1197
  • Primary Citation of Related Structures:  
    7C4B, 7C4C, 7C42, 7C43, 7C47, 7C45

  • PubMed Abstract: 
  • Infection with kinetoplastid parasites, including Trypanosoma brucei (T. brucei), Trypanosoma cruzi (T. cruzi) and Leishmania can cause serious disease in humans. Like other kinetoplastid species, mRNAs of these disease-causing parasites must undergo posttranscriptional editing in order to be functional ...

    Infection with kinetoplastid parasites, including Trypanosoma brucei (T. brucei), Trypanosoma cruzi (T. cruzi) and Leishmania can cause serious disease in humans. Like other kinetoplastid species, mRNAs of these disease-causing parasites must undergo posttranscriptional editing in order to be functional. mRNA editing is directed by gRNAs, a large group of small RNAs. Similar to mRNAs, gRNAs are also precisely regulated. In T. brucei, overexpression of RNase D ribonuclease (TbRND) leads to substantial reduction in the total gRNA population and subsequent inhibition of mRNA editing. However, the mechanisms regulating gRNA binding and cleavage by TbRND are not well defined. Here, we report a thorough structural study of TbRND. Besides Apo- and NMP-bound structures, we also solved one TbRND structure in complexed with single-stranded RNA. In combination with mutagenesis and in vitro cleavage assays, our structures indicated that TbRND follows the conserved two-cation-assisted mechanism in catalysis. TbRND is a unique RND member, as it contains a ZFD domain at its C-terminus. In addition to T. brucei, our studies also advanced our understanding on the potential gRNA degradation pathway in T. cruzi, Leishmania, as well for as other disease-associated parasites expressing ZFD-containing RNDs.


    Organizational Affiliation

    Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CCHC-type domain-containing protein A302Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb09.211.3670
Find proteins for Q38DE2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38DE2 
Go to UniProtKB:  Q38DE2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')D12synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    A
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    CA
    Query on CA

    Download Ideal Coordinates CCD File 
    A, D
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.77 Å
    • R-Value Free: 0.221 
    • R-Value Work: 0.193 
    • R-Value Observed: 0.194 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 44.449α = 90
    b = 65.843β = 90
    c = 99.914γ = 90
    Software Package:
    Software NamePurpose
    HKL-3000data scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-3000data reduction
    HKL2Mapphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2020-05-15 
    • Released Date: 2021-04-07 
    • Deposition Author(s): Gao, Y.Q., Gan, J.H.

    Funding OrganizationLocationGrant Number
    Ministry of Science and Technology (MoST, China)China2019FY101500

    Revision History  (Full details and data files)

    • Version 1.0: 2021-04-07
      Type: Initial release