Crystal Structure of the S. pombe Peptidase Homology Domain of FACT complex subunit Spt16 (form A)

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module

Stuwe, T.Hothorn, M.Lejeune, E.Rybin, V.Bortfeld, M.Scheffzek, K.Ladurner, A.G.

(2008) Proc Natl Acad Sci U S A 105: 8884-8889

  • DOI: https://doi.org/10.1073/pnas.0712293105
  • Primary Citation of Related Structures:  
    3CB5, 3CB6

  • PubMed Abstract: 

    The FACT complex is a conserved cofactor for RNA polymerase II elongation through nucleosomes. FACT bears histone chaperone activity and contributes to chromatin integrity. However, the molecular mechanisms behind FACT function remain elusive. Here we report biochemical, structural, and mutational analyses that identify the peptidase homology domain of the Schizosaccharomyces pombe FACT large subunit Spt16 (Spt16-N) as a binding module for histones H3 and H4. The 2.1-A crystal structure of Spt16-N reveals an aminopeptidase P fold whose enzymatic activity has been lost. Instead, the highly conserved fold directly binds histones H3-H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails. Mutations within a conserved surface pocket in Spt16-N or posttranslational modification of the histone H4 tail reduce interaction in vitro, whereas the globular domains of H3-H4 and the H3 tail bind distinct Spt16-N surfaces. Our analysis suggests that the N-terminal domain of Spt16 may add to the known H2A-H2B chaperone activity of FACT by including a H3-H4 tail and H3-H4 core binding function mediated by the N terminus of Spt16. We suggest that these interactions may aid FACT-mediated nucleosome reorganization events.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunit spt16
A, B
444Schizosaccharomyces pombeMutation(s): 0 
Gene Names: spt16
Find proteins for O94267 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94267 
Go to UniProtKB:  O94267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94267
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B3P

Download Ideal Coordinates CCD File 
C11 H26 N2 O6
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.07α = 90
b = 101.65β = 90
c = 103.51γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance