6BHH | pdb_00006bhh

Crystal structure of SETDB1 with a modified H3 peptide

• PDB DOI: https://doi.org/10.2210/pdb6BHH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-10-30 Released: 2017-11-22 
• Deposition Author(s): Qin, S., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.237 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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

• PubMed: 29234025 
• DOI: https://doi.org/10.1038/s41467-017-02259-9
• Primary Citation 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. 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.

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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.
Life Science Research Center, Southern University of Science and Technology, 518055, Shenzhen, China.
Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada. [e-mail].
Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada. [e-mail].
Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.59 kDa 
• Atom Count: 2,010 
• Modeled Residue Count: 221 
• Deposited Residue Count: 257 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	A	239	Homo sapiens	Mutation(s): 1  Gene Names: SETDB1, KIAA0067, KMT1E 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 GTEx:  ENSG00000143379

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	B	18	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNX	AA [auth A], BA [auth A], CA [auth A], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], 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

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS
MLY	B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.237 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36BHH

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.799	α = 90
b = 71.804	β = 104.42
c = 52.544	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Qin, S., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2018-01-03
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection