2V3M | pdb_00002v3m

Structure of the Gar1 domain of NAf1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 
    0.287 (Depositor) 
  • R-Value Work: 
    0.257 (Depositor) 
  • R-Value Observed: 
    0.259 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The Box H/Aca Rnp Assembly Factor Naf1P Contains a Domain Homologous to Gar1P Mediating its Interaction with Cbf5P.

Leulliot, N.Godin, K.S.Hoareau-Aveilla, C.Quevillon-Cheruel, S.Varani, G.Henry, Y.Van Tilbeurgh, H.

(2007) J Mol Biology 371: 1338

  • DOI: https://doi.org/10.1016/j.jmb.2007.06.031
  • Primary Citation Related Structures: 
    2V3M

  • PubMed Abstract: 

    Naf1 is an essential protein involved in the maturation of box H/ACA ribonucleoproteins, a group of particles required for ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis. Naf1 participates in the assembly of the RNP at transcription sites and in the nuclear trafficking of the complex. The crystal structure of a domain of yeast Naf1p, Naf1Delta1p, reveals a striking structural homology with the core domain of archaeal Gar1, an essential protein component of the mature RNP; it suggests that Naf1p and Gar1p have a common binding site on the enzymatic protein component of the particle, Cbf5p. We propose that Naf1p is a competitive binder for Cbf5p, which is replaced by Gar1p during maturation of the H/ACA particle. The exchange of Naf1p by Gar1p might be prompted by external factors that alter the oligomerisation state of Naf1p and Gar1p. The structural homology with Gar1 suggests that the function of Naf1 involves preventing non-cognate RNAs from being loaded during transport of the particle by inducing a non-productive conformation of Cbf5.


  • Organizational Affiliation
    • Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Bât 430, Université de Paris-Sud, 91405 Orsay Cedex, France. nicolas.leulliot@u-psud.fr

Macromolecule Content 

  • Total Structure Weight: 92.08 kDa 
  • Atom Count: 4,576 
  • Modeled Residue Count: 567 
  • Deposited Residue Count: 786 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAF1
A, B, C, D, E
A, B, C, D, E, F
131Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53919 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53919 
Go to UniProtKB:  P53919
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53919
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.287 (Depositor) 
  • R-Value Work:  0.257 (Depositor) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.534α = 90
b = 103.534β = 90
c = 109.031γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SHELXDphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2011-08-17
    Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary