3MP6

Complex Structure of Sgf29 and dimethylated H3K4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1038/emboj.2011.193
  • Primary Citation of Related Structures:  

  • 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 Tu ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29
A
522Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Escherichia coli (strain K12)
This entity is chimeric
Mutation(s): 0 
Gene Names: SGF29, malE
Find proteins for P25554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SGF29
Go to UniProtKB:  P25554
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3K4me2 peptide
P
4Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
P
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.169α = 90.00
b = 85.333β = 90.00
c = 119.313γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MAR345dtbdata collection
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-12
    Type: Database references
  • Version 1.3: 2017-06-21
    Type: Advisory, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2017-11-08
    Type: Refinement description