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 

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This is version 1.3 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: https://doi.org/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 detailed mechanism is not understood ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Xenopus laevisMutation(s): 0 
UniProt
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UniProt GroupP62799
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H123Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificK331Homo sapiensMutation(s): 0 
Gene Names: DOT1L, KIAA1814, KMT4
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
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Find proteins for Q8TEK3 (Homo sapiens)
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PHAROS:  Q8TEK3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BL76Homo sapiensMutation(s): 1 
Gene Names: UBB
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PHAROS:  P0CG47
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)I146synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (146-MER)J146synthetic construct
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
M [auth K]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  6O96 Ki: min: 160, max: 270 (nM) from 2 assay(s)
Kd: min: 150, max: 360 (nM) from 2 assay(s)
IC50: min: 220, max: 600 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX1.14

Structure Validation

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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  (Full details and data files)

  • 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
  • Version 1.3: 2023-02-01
    Changes: Database references, Refinement description