3QTM | pdb_00003qtm

Structure of S. pombe nuclear import adaptor Nro1 (Space group P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3QTM

This is version 1.3 of the entry. See complete history

Literature

Structural and functional analysis of Nro1/Ett1: a protein involved in translation termination in S. cerevisiae and in O2-mediated gene control in S. pombe

Rispal, D.Henri, J.van Tilbeurgh, H.Graille, M.Seraphin, B.

(2011) RNA 17: 1213-1224

  • DOI: https://doi.org/10.1261/rna.2697111
  • Primary Citation Related Structures: 
    3QTM, 3QTN

  • PubMed Abstract: 

    In Saccharomyces cerevisiae, the putative 2-OG-Fe(II) dioxygenase Tpa1 and its partner Ett1 have been shown to impact mRNA decay and translation. Hence, inactivation of these factors was shown to influence stop codon read-though. In addition, Tpa1 represses, by an unknown mechanism, genes regulated by Hap1, a transcription factor involved in the response to levels of heme and O(2). The Schizosaccharomyces pombe orthologs of Tpa1 and Ett1, Ofd1, and its partner Nro1, respectively, have been shown to regulate the stability of the Sre1 transcription factor in response to oxygen levels. To gain insight into the function of Nro1/Ett1, we have solved the crystal structure of the S. pombe Nro1 protein deleted of its 54 N-terminal residues. Nro1 unexpectedly adopts a Tetratrico Peptide Repeat (TPR) fold, a motif often responsible for protein or peptide binding. Two ligands, a sulfate ion and an unknown molecule, interact with a cluster of highly conserved amino acids on the protein surface. Mutation of these residues demonstrates that these ligand binding sites are essential for Ett1 function in S. cerevisiae, as investigated by assaying for efficient translation termination.


  • Organizational Affiliation
    • CNRS UMR7104, Inserm U964, Université de Strasbourg, Strasbourg, Illkirch F-67000, France.

Macromolecule Content 

  • Total Structure Weight: 80.08 kDa 
  • Atom Count: 5,892 
  • Modeled Residue Count: 657 
  • Deposited Residue Count: 692 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein C4B3.07
A, B
346Schizosaccharomyces pombeMutation(s): 0 
Gene Names: SPCC4B3.07
UniProt
Find proteins for Q9USJ7 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9USJ7 
Go to UniProtKB:  Q9USJ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9USJ7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.93α = 90
b = 107.84β = 102.29
c = 101.79γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Structure summary
  • Version 1.2: 2018-01-03
    Changes: Structure summary
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary