6NQA

Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 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

Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L.

Worden, E.J.Hoffmann, N.A.Hicks, C.W.Wolberger, C.

(2019) Cell 176: 1490-1501.e12

  • DOI: https://doi.org/10.1016/j.cell.2019.02.002
  • Primary Citation of Related Structures:  
    6NJ9, 6NOG, 6NQA

  • PubMed Abstract: 

    Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.


  • Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth F],
L [auth B]
102Xenopus laevisMutation(s): 0 
UniProt
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UniProt GroupP62799
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1D [auth G],
K [auth C]
129Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1E [auth H],
J [auth D]
122Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificF [auth K]416Homo sapiensMutation(s): 0 
Gene Names: DOT1LKIAA1814KMT4
EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinG [auth L]80Homo sapiensMutation(s): 1 
Gene Names: UBC
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Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2H [auth E],
I [auth A]
135Xenopus laevisMutation(s): 4 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
601 DNA Strand 1A [auth I]146synthetic construct
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Entity ID: 2
MoleculeChains LengthOrganismImage
601 DNA Strand 2B [auth J]146synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
M [auth K]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NLE
Query on NLE
H [auth E],
I [auth A]
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

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 StatesGM095822

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence