3U28

Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


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Literature

Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase

Li, S.Duan, J.Li, D.Yang, B.Dong, M.Ye, K.

(2011) Genes Dev 25: 2409-2421

  • DOI: 10.1101/gad.175299.111
  • Primary Citation of Related Structures:  
    3U28

  • PubMed Abstract: 
  • Box H/ACA ribonucleoprotein particles (RNPs) mediate pseudouridine synthesis, ribosome formation, and telomere maintenance. The structure of eukaryotic H/ACA RNPs remains poorly understood. We reconstituted functional Saccharomyces cerevisiae H/ACA RNPs with recombinant proteins Cbf5, Nop10, Gar1, and Nhp2 and a two-hairpin H/ACA RNA; determined the crystal structure of a Cbf5, Nop10, and Gar1 ternary complex at 1 ...

    Box H/ACA ribonucleoprotein particles (RNPs) mediate pseudouridine synthesis, ribosome formation, and telomere maintenance. The structure of eukaryotic H/ACA RNPs remains poorly understood. We reconstituted functional Saccharomyces cerevisiae H/ACA RNPs with recombinant proteins Cbf5, Nop10, Gar1, and Nhp2 and a two-hairpin H/ACA RNA; determined the crystal structure of a Cbf5, Nop10, and Gar1 ternary complex at 1.9 Å resolution; and analyzed the structure-function relationship of the yeast complex. Although eukaryotic H/ACA RNAs have a conserved two-hairpin structure, isolated single-hairpin RNAs are also active in guiding pseudouridylation. Nhp2, unlike its archaeal counterpart, is largely dispensable for the activity, reflecting a functional adaptation of eukaryotic H/ACA RNPs to the variable RNA structure that Nhp2 binds. The N-terminal extension of Cbf5, a hot spot for dyskeratosis congenita mutation, forms an extra structural layer on the PUA domain. Gar1 is distinguished from the assembly factor Naf1 by containing a C-terminal extension that controls substrate turnover and the Gar1-Naf1 exchange during H/ACA RNP maturation. Our results reveal significant novel features of eukaryotic H/ACA RNPs.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 4 A400Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CBF5YLR175WL9470.11
EC: 5.4.99
Find proteins for P33322 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33322 
Go to UniProtKB:  P33322
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 3 B58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP10YHR072W-A
Find proteins for Q6Q547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q6Q547 
Go to UniProtKB:  Q6Q547
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 1 C114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GAR1YHR089C
Find proteins for P28007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28007 
Go to UniProtKB:  P28007
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.413α = 90
b = 59.386β = 90
c = 169.212γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2011-10-02 
  • Released Date: 2011-12-14 
  • Deposition Author(s): Ye, K., Li, S.

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release