6JMA

cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase.

Jang, S.Kang, C.Yang, H.S.Jung, T.Hebert, H.Chung, K.Y.Kim, S.J.Hohng, S.Song, J.J.

(2019) Genes Dev 33: 620-625

  • DOI: https://doi.org/10.1101/gad.323790.118
  • Primary Citation of Related Structures:  
    6JM9, 6JMA

  • PubMed Abstract: 

    DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Furthermore, the structures combined with single-molecule FRET experiments show that H2B ubiquitination enhances a noncatalytic function of the DOT1L-destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L.


  • Organizational Affiliation

    Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2C [auth A],
G [auth E]
98Xenopus laevisMutation(s): 0 
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UniProt GroupP84233
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
87Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]
116Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj
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Find proteins for Q6AZJ8 (Xenopus laevis)
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UniProt GroupQ6AZJ8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1F [auth D],
J [auth H]
94Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificK [auth X]328Homo sapiensMutation(s): 0 
Gene Names: DOT1L
EC: 2.1.1.43
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Find proteins for Q8TEK3 (Homo sapiens)
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PHAROS:  Q8TEK3
GTEx:  ENSG00000104885 
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UniProt GroupQ8TEK3
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinL [auth Y]76Homo sapiensMutation(s): 0 
Gene Names: UBB
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PHAROS:  P0CG47
GTEx:  ENSG00000170315 
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA I&JA [auth I],
B [auth J]
114synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
M [auth X]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2016R1A2B3006293
National Research Foundation (Korea)Korea, Republic OfNRF-2016K1A1A2912057
National Research Foundation (Korea)Korea, Republic OfNRF- 2016H1A2A1908806

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other