3HAY

Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.99 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.323 
  • R-Value Observed: 0.325 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.

Duan, J.Li, L.Lu, J.Wang, W.Ye, K.

(2009) Mol Cell 34: 427-439

  • DOI: 10.1016/j.molcel.2009.05.005
  • Primary Citation of Related Structures:  
    3HAX, 3HAY

  • PubMed Abstract: 
  • H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts ...

    H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts. Substrate binding leads to a reorganization of a preset pseudouridylation pocket and an adaptive movement of the PUA domain and the lower stem of the H/ACA RNA. Moreover, a thumb loop flips from the Gar1-bound state in the substrate-free RNP structure to tightly associate with the substrate. Mutagenesis and enzyme kinetics analysis suggest a critical role of Gar1 and the thumb in substrate turnover, particularly in product release. Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5.


    Organizational Affiliation

    College of Life Sciences, Peking University, Beijing, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable tRNA pseudouridine synthase BA346Pyrococcus furiosusMutation(s): 0 
Gene Names: truBPF1785
EC: 5.4.99 (PDB Primary Data), 5.4.99.25 (UniProt)
UniProt
Find proteins for Q7LWY0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q7LWY0 
Go to UniProtKB:  Q7LWY0
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nucleolar rnp gar1-like proteinB104Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1791
UniProt
Find proteins for Q8U029 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U029 
Go to UniProtKB:  Q8U029
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein Nop10C60Pyrococcus furiosusMutation(s): 1 
Gene Names: PF1141
UniProt
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1R4 
Go to UniProtKB:  Q8U1R4
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeD130Pyrococcus furiosusMutation(s): 0 
Gene Names: rpl7aePF1367
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U160 
Go to UniProtKB:  Q8U160
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
H/ACA RNAE71N/A
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 6
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'F14N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    G [auth C]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 4.99 Å
    • R-Value Free: 0.367 
    • R-Value Work: 0.323 
    • R-Value Observed: 0.325 
    • Space Group: P 64 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 189.518α = 90
    b = 189.518β = 90
    c = 279.045γ = 120
    Software Package:
    Software NamePurpose
    MOLREPphasing
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    • Deposited Date: 2009-05-03 
    • Released Date: 2009-06-23 
    • Deposition Author(s): Ye, K.

    Revision History  (Full details and data files)

    • Version 1.0: 2009-06-23
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance