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 1.3 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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
123Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specific331Homo sapiensMutation(s): 0 
Gene Names: DOT1LKIAA1814KMT4
EC: 2.1.1.43
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Find proteins for Q8TEK3 (Homo sapiens)
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PHAROS:  Q8TEK3
GTEx:  ENSG00000104885 
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UniProt GroupQ8TEK3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-B76Homo sapiensMutation(s): 1 
Gene Names: UBB
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Find proteins for P0CG47 (Homo sapiens)
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PHAROS:  P0CG47
GTEx:  ENSG00000170315 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (146-MER)146synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (146-MER)146synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / 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
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