6NZO

Set2 bound to nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nucleosome and ubiquitin position Set2 to methylate H3K36.

Bilokapic, S.Halic, M.

(2019) Nat Commun 10: 3795-3795

  • DOI: 10.1038/s41467-019-11726-4
  • Primary Citation of Related Structures:  
    6NZO, 6PX1, 6PX3

  • PubMed Abstract: 
  • Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me ...

    Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me are poorly understood. Set2 enzymes show spurious activity on histones and histone tails, and it is unknown how they obtain specificity to methylate H3K36 on the nucleosome. In this study, we present 3.8 Å cryo-EM structure of Set2 bound to the mimic of H2B ubiquitinated nucleosome. Our structure shows that Set2 makes extensive interactions with the H3 αN, the H3 tail, the H2A C-terminal tail and stabilizes DNA in the unwrapped conformation, which positions Set2 to specifically methylate H3K36. Moreover, we show that ubiquitin contributes to Set2 positioning on the nucleosome and stimulates the methyltransferase activity. Notably, our structure uncovers interfaces that can be targeted by small molecules for development of future cancer therapies.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA. Mario.Halic@stjude.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3AE136Xenopus laevisMutation(s): 1 
Gene Names: XELAEV_18002543mgh3-5h3f3c
Find proteins for P02302 (Xenopus laevis)
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Go to UniProtKB:  P02302
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Go to UniProtKB:  P62799
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40,Histone H2ACG221Saccharomyces cerevisiae S288CXenopus laevis
This entity is chimeric
Mutation(s): 0 
Gene Names: RPL40BUBI2YKR094C
Find proteins for P06897 (Xenopus laevis)
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Go to UniProtKB:  P06897
Find proteins for P0CH09 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P0CH09
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1DH123Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
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Go to UniProtKB:  P02281
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferaseS939Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0025760
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.359 (UniProt)
Find proteins for G0S676 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (149-MER)I149synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (149-MER)J149synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references