6BHH

Crystal structure of SETDB1 with a modified H3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1.

Jurkowska, R.Z.Qin, S.Kungulovski, G.Tempel, W.Liu, Y.Bashtrykov, P.Stiefelmaier, J.Jurkowski, T.P.Kudithipudi, S.Weirich, S.Tamas, R.Wu, H.Dombrovski, L.Loppnau, P.Reinhardt, R.Min, J.Jeltsch, A.

(2017) Nat Commun 8: 2057-2057

  • DOI: 10.1038/s41467-017-02259-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. C ...

    SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2. Mutations in the K14ac/K9me binding sites change the sub-nuclear localization of 3TD. ChIP-seq analyses show that SETDB1 is enriched at H3K9me3 regions and K9me3/K14ac is enriched at SETDB1 binding sites overlapping with LINE elements, suggesting that recruitment of the SETDB1 complex to K14ac/K9me regions has a role in silencing of active genomic regions.


    Organizational Affiliation

    Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada. jr.min@utoronto.ca.,Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada. jr.min@utoronto.ca.,Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany. albert.jeltsch@ibc.uni-stuttgart.de.,Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.,Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829, Köln, Germany.,Life Science Research Center, Southern University of Science and Technology, 518055, Shenzhen, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SETDB1
A
239Homo sapiensMutation(s): 1 
Gene Names: SETDB1 (ESET, KIAA0067, KMT1E)
EC: 2.1.1.-
Find proteins for Q15047 (Homo sapiens)
Go to Gene View: SETDB1
Go to UniProtKB:  Q15047
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
B
18Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

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ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
MLY
Query on MLY
B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 37.799α = 90.00
b = 71.804β = 104.42
c = 52.544γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references