6MAK

HBO1 is required for the maintenance of leukaemia stem cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

HBO1 is required for the maintenance of leukaemia stem cells.

MacPherson, L.Anokye, J.Yeung, M.M.Lam, E.Y.N.Chan, Y.C.Weng, C.F.Yeh, P.Knezevic, K.Butler, M.S.Hoegl, A.Chan, K.L.Burr, M.L.Gearing, L.J.Willson, T.Liu, J.Choi, J.Yang, Y.Bilardi, R.A.Falk, H.Nguyen, N.Stupple, P.A.Peat, T.S.Zhang, M.de Silva, M.Carrasco-Pozo, C.Avery, V.M.Khoo, P.S.Dolezal, O.Dennis, M.L.Nuttall, S.Surjadi, R.Newman, J.Ren, B.Leaver, D.J.Sun, Y.Baell, J.B.Dovey, O.Vassiliou, G.S.Grebien, F.Dawson, S.J.Street, I.P.Monahan, B.J.Burns, C.J.Choudhary, C.Blewitt, M.E.Voss, A.K.Thomas, T.Dawson, M.A.

(2020) Nature 577: 266-270

  • DOI: https://doi.org/10.1038/s41586-019-1835-6
  • Primary Citation of Related Structures:  
    6MAJ, 6MAK

  • PubMed Abstract: 

    Acute myeloid leukaemia (AML) is a heterogeneous disease characterized by transcriptional dysregulation that results in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, but most show only modest efficacy owing to an inability to effectively eradicate leukaemia stem cells (LSCs) 1 . Here, to specifically identify novel dependencies in LSCs, we screened a bespoke library of small hairpin RNAs that target chromatin regulators in a unique ex vivo mouse model of LSCs. We identify the MYST acetyltransferase HBO1 (also known as KAT7 or MYST2) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance. Using CRISPR domain screening and quantitative mass spectrometry, we identified the histone acetyltransferase domain of HBO1 as being essential in the acetylation of histone H3 at K14. H3 acetylated at K14 (H3K14ac) facilitates the processivity of RNA polymerase II to maintain the high expression of key genes (including Hoxa9 and Hoxa10) that help to sustain the functional properties of LSCs. To leverage this dependency therapeutically, we developed a highly potent small-molecule inhibitor of HBO1 and demonstrate its mode of activity as a competitive analogue of acetyl-CoA. Inhibition of HBO1 phenocopied our genetic data and showed efficacy in a broad range of human cell lines and primary AML cells from patients. These biological, structural and chemical insights into a therapeutic target in AML will enable the clinical translation of these findings.


  • Organizational Affiliation

    Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT7279Homo sapiensMutation(s): 0 
Gene Names: KAT7HBO1HBOaMYST2
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for O95251 (Homo sapiens)
Explore O95251 
Go to UniProtKB:  O95251
PHAROS:  O95251
GTEx:  ENSG00000136504 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95251
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BRD1 protein52Homo sapiensMutation(s): 0 
Gene Names: BRD1
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens)
Explore O95696 
Go to UniProtKB:  O95696
PHAROS:  O95696
GTEx:  ENSG00000100425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95696
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download Ideal Coordinates CCD File 
D [auth A]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.628α = 90
b = 39.026β = 99.59
c = 107.765γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references