6O96

Dot1L bound to the H2BK120 Ubiquitinated nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination.

Valencia-Sanchez, M.I.De Ioannes, P.Wang, M.Vasilyev, N.Chen, R.Nudler, E.Armache, J.P.Armache, K.J.

(2019) Mol Cell 74: 1010

  • DOI: 10.1016/j.molcel.2019.03.029
  • Primary Citation of Related Structures:  
    6O96

  • PubMed Abstract: 
  • The essential histone H3 lysine 79 methyltransferase Dot1L regulates transcription and genomic stability and is deregulated in leukemia. The activity of Dot1L is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120Ub); however, the det ...

    The essential histone H3 lysine 79 methyltransferase Dot1L regulates transcription and genomic stability and is deregulated in leukemia. The activity of Dot1L is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120Ub); however, the detailed mechanism is not understood. We report cryo-EM structures of human Dot1L bound to (1) H2BK120Ub and (2) unmodified nucleosome substrates at 3.5 Å and 4.9 Å, respectively. Comparison of both structures, complemented with biochemical experiments, provides critical insights into the mechanism of Dot1L stimulation by H2BK120Ub. Both structures show Dot1L binding to the same extended surface of the histone octamer. In yeast, this surface is used by silencing proteins involved in heterochromatin formation, explaining the mechanism of their competition with Dot1. These results provide a strong foundation for understanding conserved crosstalk between histone modifications found at actively transcribed genes and offer a general model of how ubiquitin might regulate the activity of chromatin enzymes.


    Organizational Affiliation

    Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA. Electronic address: karim-jean.armache@nyulangone.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2 AE135Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 BF103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A CG130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1 DH123Xenopus laevisMutation(s): 2 
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specific K331Homo 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)
Explore Q8TEK3 
Go to UniProtKB:  Q8TEK3
NIH Common Fund Data Resources
PHAROS:  Q8TEK3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B L76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)I146synthetic construct
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (146-MER)J146synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
K
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM115882-03
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127267
Other privateUnited StatesDavid and Lucile Packard Foundation

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other