6JMA

cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1101/gad.323790.118
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, S-141 52 Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 52 Huddinge, Sweden.,Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea.,School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea.,Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
98Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
87Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
116Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj (LOC494591)
Find proteins for Q6AZJ8 (Xenopus laevis)
Go to UniProtKB:  Q6AZJ8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
94Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-79 specific
X
328Homo sapiensMutation(s): 0 
Gene Names: DOT1L (KIAA1814, KMT4)
EC: 2.1.1.43
Find proteins for Q8TEK3 (Homo sapiens)
Go to Gene View: DOT1L
Go to UniProtKB:  Q8TEK3
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
Y
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 1
MoleculeChainsLengthOrganism
DNA I&JI,J114synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
X
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-07 
  • Released Date: 2019-05-15 
  • Deposition Author(s): Jang, S., Song, J.J.

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 

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