3U28 | pdb_00003u28

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 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3U28

This is version 1.1 of the entry. See complete history

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: https://doi.org/10.1101/gad.175299.111
  • Primary Citation 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 1.9 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.

Macromolecule Content 

  • Total Structure Weight: 64.25 kDa 
  • Atom Count: 4,028 
  • Modeled Residue Count: 475 
  • Deposited Residue Count: 572 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 4400Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CBF5
EC: 5.4.99
UniProt
Find proteins for P33322 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33322 
Go to UniProtKB:  P33322
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33322
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 358Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP10
UniProt
Find proteins for Q6Q547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q6Q547 
Go to UniProtKB:  Q6Q547
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Q547
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 1114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GAR1
UniProt
Find proteins for P28007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28007 
Go to UniProtKB:  P28007
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28007
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
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

  • 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
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description