3CB5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.USA 105: 8884-8889

  • DOI: 10.1073/pnas.0712293105
  • Primary Citation of Related Structures:  

  • 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 w ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FACT complex subunit spt16
A, B
444Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: spt16
Find proteins for O94267 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94267
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download SDF File 
Download CCD File 
A
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 97.070α = 90.00
b = 101.650β = 90.00
c = 103.510γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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