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:  
    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 ...

    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

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2C [auth A],
G [auth E]		98Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84233
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]		87Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62799
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]		116Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, h2ac14.L, h2ac14, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
Explore Q6AZJ8 
Go to UniProtKB:  Q6AZJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6AZJ8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1F [auth D],
J [auth H]		94Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02281
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificK [auth X]328Homo sapiensMutation(s): 0 
Gene Names: DOT1L, KIAA1814, KMT4
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens)
Explore Q8TEK3 
Go to UniProtKB:  Q8TEK3
PHAROS:  Q8TEK3
GTEx:  ENSG00000104885 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TEK3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinL [auth Y]76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA I&JA [auth I],
B [auth J]		114synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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		 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



View more in-depth experimental data

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  (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