6BHE

Crystal structure of SETDB1 with a modified H3 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 

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: https://doi.org/10.1038/s41467-017-02259-9
  • Primary Citation of Related Structures:  
    6BHD, 6BHE, 6BHG, 6BHH, 6BHI

  • 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. 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 ...

    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. albert.jeltsch@ibc.uni-stuttgart.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETDB1239Homo sapiensMutation(s): 0 
Gene Names: SETDB1, KIAA0067, KMT1E, ESET
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.366 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens)
Explore Q15047 
Go to UniProtKB:  Q15047
PHAROS:  Q15047
Entity Groups  
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UniProt GroupQ15047
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.118Homo sapiensMutation(s): 2 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX
Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
C [auth A]
CA [auth A]
D [auth A]
AA [auth A],
BA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
EA [auth A],
F [auth A],
FA [auth A],
G [auth A],
GA [auth A],
H [auth A],
HA [auth A],
I [auth A],
IA [auth A],
J [auth A],
JA [auth A],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.051α = 90
b = 71.372β = 104.23
c = 52.055γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references