6E0T | pdb_00006e0t

C-terminal domain of Fission Yeast OFD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.244 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6E0T

This is version 1.1 of the entry. See complete history

Literature

The hypoxic regulator of sterol synthesis nro1 is a nuclear import adaptor.

Yeh, T.L.Lee, C.Y.Amzel, L.M.Espenshade, P.J.Bianchet, M.A.

(2011) Structure 19: 503-514

  • DOI: https://doi.org/10.1016/j.str.2011.01.017
  • Primary Citation Related Structures: 
    3MSV, 6E0T

  • PubMed Abstract: 

    Fission yeast protein Sre1, the homolog of the mammalian sterol regulatory element-binding protein (SREBP), is a hypoxic transcription factor required for sterol homeostasis and low-oxygen growth. Nro1 regulates the stability of the N-terminal transcription factor domain of Sre1 (Sre1N) by inhibiting the action of the prolyl 4-hydroxylase-like Ofd1 in an oxygen-dependent manner. The crystal structure of Nro1 determined at 2.2 Å resolution shows an all-α-helical fold that can be divided into two domains: a small N-terminal domain, and a larger C-terminal HEAT-repeat domain. Follow-up studies showed that Nro1 defines a new class of nuclear import adaptor that functions both in Ofd1 nuclear localization and in the oxygen-dependent inhibition of Ofd1 to control the hypoxic response.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205, USA.

Macromolecule Content 

  • Total Structure Weight: 30.37 kDa 
  • Atom Count: 2,168 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 265 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prolyl 3,4-dihydroxylase ofd1A [auth X]265Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ofd1SPBC6B1.08c
EC: 1.14.11
UniProt
Find proteins for Q11120 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q11120 
Go to UniProtKB:  Q11120
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ11120
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.244 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.085α = 90
b = 106.717β = 90
c = 64.649γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references