Crystal structure of the SGF29 in complex with H3K4me3

Experimental Data Snapshot

  • Resolution: 1.26 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation.

Bian, C.Xu, C.Ruan, J.Lee, K.K.Burke, T.L.Tempel, W.Barsyte, D.Li, J.Wu, M.Zhou, B.O.Fleharty, B.E.Paulson, A.Allali-Hassani, A.Zhou, J.Q.Mer, G.Grant, P.A.Workman, J.L.Zang, J.Min, J.

(2011) EMBO J 30: 2829-2842

  • DOI: https://doi.org/10.1038/emboj.2011.193
  • Primary Citation of Related Structures:  
    3LX7, 3ME9, 3MEA, 3MET, 3MEU, 3MEV, 3MEW, 3MP1, 3MP6, 3MP8

  • PubMed Abstract: 

    The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an important chromatin modifying complex that can both acetylate and deubiquitinate histones. Sgf29 is a novel component of the SAGA complex. Here, we report the crystal structures of the tandem Tudor domains of Saccharomyces cerevisiae and human Sgf29 and their complexes with H3K4me2 and H3K4me3 peptides, respectively, and show that Sgf29 selectively binds H3K4me2/3 marks. Our crystal structures reveal that Sgf29 harbours unique tandem Tudor domains in its C-terminus. The tandem Tudor domains in Sgf29 tightly pack against each other face-to-face with each Tudor domain harbouring a negatively charged pocket accommodating the first residue alanine and methylated K4 residue of histone H3, respectively. The H3A1 and K4me3 binding pockets and the limited binding cleft length between these two binding pockets are the structural determinants in conferring the ability of Sgf29 to selectively recognize H3K4me2/3. Our in vitro and in vivo functional assays show that Sgf29 recognizes methylated H3K4 to recruit the SAGA complex to its targets sites and mediates histone H3 acetylation, underscoring the importance of Sgf29 in gene regulation.

  • Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Anhui, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 29 homolog180Homo sapiensMutation(s): 0 
Gene Names: CCDC101SGF29
UniProt & NIH Common Fund Data Resources
Find proteins for Q96ES7 (Homo sapiens)
Explore Q96ES7 
Go to UniProtKB:  Q96ES7
GTEx:  ENSG00000176476 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96ES7
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H311Xenopus laevisMutation(s): 0 
Find proteins for Q92133 (Xenopus laevis)
Explore Q92133 
Go to UniProtKB:  Q92133
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92133
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on M3L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.385α = 90
b = 41.425β = 121.39
c = 52.527γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-03
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description