2V3M

Structure of the Gar1 domain of NAf1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.Biol. 371: 1338

  • DOI: 10.1016/j.jmb.2007.06.031

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAF1
A, B, C, D, E, F
131Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NAF1
Find proteins for P53919 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NAF1
Go to UniProtKB:  P53919
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.534α = 90.00
b = 103.534β = 90.00
c = 109.031γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
REFMACrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2011-08-17
    Type: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance