5GPD

Crystal structure of the binding domain of SREBP from fission yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization

Gong, X.Qian, H.Shao, W.Li, J.Wu, J.Liu, J.J.Li, W.Wang, H.W.Espenshade, P.Yan, N.

(2016) Cell Res 26: 1197-1211

  • DOI: https://doi.org/10.1038/cr.2016.123
  • Primary Citation of Related Structures:  
    5GPD, 5GRS

  • PubMed Abstract: 

    Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sterol regulatory element-binding protein 1
A, B
252Schizosaccharomyces pombe 972h-Mutation(s): 2 
Gene Names: sre1SPBC19C2.09
UniProt
Find proteins for Q9UUD1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UUD1 
Go to UniProtKB:  Q9UUD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUD1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.903α = 90
b = 96.903β = 90
c = 151.595γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2015CB9101012014, ZX09507003006
National Natural Science Foundation of ChinaChinaproject 31321062 and 81590761

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references