5J9S

ENL YEATS in complex with histone H3 acetylation at K27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.702 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia

Wan, L.Wen, H.Li, Y.Lyu, J.Xi, Y.Hoshii, T.Joseph, J.K.Wang, X.Loh, Y.E.Erb, M.A.Souza, A.L.Bradner, J.E.Shen, L.Li, W.Li, H.Allis, C.D.Armstrong, S.A.Shi, X.

(2017) Nature 543: 265-269

  • DOI: 10.1038/nature21687

  • PubMed Abstract: 
  • Cancer cells are characterized by aberrant epigenetic landscapes and often exploit chromatin machinery to activate oncogenic gene expression programs. Recognition of modified histones by 'reader' proteins constitutes a key mechanism underlying these ...

    Cancer cells are characterized by aberrant epigenetic landscapes and often exploit chromatin machinery to activate oncogenic gene expression programs. Recognition of modified histones by 'reader' proteins constitutes a key mechanism underlying these processes; therefore, targeting such pathways holds clinical promise, as exemplified by the development of bromodomain and extra-terminal (BET) inhibitors. We recently identified the YEATS domain as an acetyl-lysine-binding module, but its functional importance in human cancer remains unknown. Here we show that the YEATS domain-containing protein ENL, but not its paralogue AF9, is required for disease maintenance in acute myeloid leukaemia. CRISPR-Cas9-mediated depletion of ENL led to anti-leukaemic effects, including increased terminal myeloid differentiation and suppression of leukaemia growth in vitro and in vivo. Biochemical and crystal structural studies and chromatin-immunoprecipitation followed by sequencing analyses revealed that ENL binds to acetylated histone H3, and co-localizes with H3K27ac and H3K9ac on the promoters of actively transcribed genes that are essential for leukaemia. Disrupting the interaction between the YEATS domain and histone acetylation via structure-based mutagenesis reduced the recruitment of RNA polymerase II to ENL-target genes, leading to the suppression of oncogenic gene expression programs. Notably, disrupting the functionality of ENL further sensitized leukaemia cells to BET inhibitors. Together, our data identify ENL as a histone acetylation reader that regulates oncogenic transcriptional programs in acute myeloid leukaemia, and suggest that displacement of ENL from chromatin may be a promising epigenetic therapy, alone or in combination with BET inhibitors, for aggressive leukaemia.


    Organizational Affiliation

    Laboratory of Chromatin Biology &Epigenetics, The Rockefeller University, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein ENL
A
155Homo sapiensMutation(s): 0 
Gene Names: MLLT1 (ENL, LTG19, YEATS1)
Find proteins for Q03111 (Homo sapiens)
Go to Gene View: MLLT1
Go to UniProtKB:  Q03111
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3K27ac peptide from Histone H3.1
B
25Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.702 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.979α = 90.00
b = 104.979β = 90.00
c = 45.128γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-04-11 
  • Released Date: 2017-03-08 
  • Deposition Author(s): Li, Y., Li, H.

Funding OrganizationLocationGrant Number
National Science Foudation pf ChinaChina91519304

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references