Crystal structure of the Bateman2 domain of yeast Snf4

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

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Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding.

Rudolph, M.J.Amodeo, G.A.Iram, S.Hong, S.P.Pirino, G.Carlson, M.Tong, L.

(2007) Structure 15: 65-74

  • DOI: https://doi.org/10.1016/j.str.2006.11.014
  • Primary Citation of Related Structures:  
    2NYC, 2NYE

  • PubMed Abstract: 

    AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals. AMP is believed to control the activity of AMPK by binding to the gamma subunit of this heterotrimeric enzyme. This subunit contains two Bateman domains, each of which is composed of a tandem pair of cystathionine beta-synthase (CBS) motifs. No structural information is currently available on this subunit, and the molecular basis for its interactions with AMP is not well understood. We report here the crystal structure at 1.9 Angstrom resolution of the Bateman2 domain of Snf4, the gamma subunit of the yeast ortholog of AMPK. The structure revealed a dimer of the Bateman2 domain, and this dimerization is supported by our light-scattering, mutagenesis, and biochemical studies. There is a prominent pocket at the center of this dimer, and most of the disease-causing mutations are located in or near this pocket.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear protein SNF4
A, B
144Saccharomyces cerevisiaeMutation(s): 5 
Gene Names: SNF4CAT3
Find proteins for P12904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P12904 
Go to UniProtKB:  P12904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12904
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.618α = 90
b = 235.618β = 90
c = 235.618γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection