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

  • 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 unmo ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2 AE98Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 BF87Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A CG116Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajh2ac14.Lh2ac14LOC494591XELAEV_18003602mg
Find proteins for Q6AZJ8 (Xenopus laevis)
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Go to UniProtKB:  Q6AZJ8
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1 DH94Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
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Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specific X328Homo sapiensMutation(s): 0 
Gene Names: DOT1LKIAA1814KMT4
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
Find proteins for Q8TEK3 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  Q8TEK3
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin Y76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  P0CG47
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA I&JI, J114synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

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

Experimental Data

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

Structure Validation

View Full Validation Report



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
    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