5YYF

Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2017-12-09 Released: 2018-11-07 
  • Deposition Author(s): Li, Y., Li, H.
  • Funding Organization(s): National Natural Science Foundation of China, CHINA ASSOCIATION FOR SCIENCE AND TECHNOLOGY

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-guided development of YEATS domain inhibitors by targeting pi-pi-pi stacking.

Li, X.Li, X.M.Jiang, Y.Liu, Z.Cui, Y.Fung, K.Y.van der Beelen, S.H.E.Tian, G.Wan, L.Shi, X.Allis, C.D.Li, H.Li, Y.Li, X.D.

(2018) Nat Chem Biol 14: 1140-1149

  • DOI: 10.1038/s41589-018-0144-y
  • Primary Citation of Related Structures:  
    5YYF

  • PubMed Abstract: 
  • Chemical probes of epigenetic 'readers' of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in normal physiology and disease pathogenesis. Here we report the development of the first class of chemical probes of YEATS domains, newly identified 'readers' of histone lysine acetylation (Kac) and crotonylation (Kcr) ...

    Chemical probes of epigenetic 'readers' of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in normal physiology and disease pathogenesis. Here we report the development of the first class of chemical probes of YEATS domains, newly identified 'readers' of histone lysine acetylation (Kac) and crotonylation (Kcr). Guided by the structural analysis of a YEATS-Kcr complex, we developed a series of peptide-based inhibitors of YEATS domains by targeting a unique π-π-π stacking interaction at the proteins' Kcr recognition site. Further structure optimization resulted in the selective inhibitors preferentially binding to individual YEATS-containing proteins including AF9 and ENL with submicromolar affinities. We demonstrate that one of the ENL YEATS-selective inhibitors, XL-13m, engages with endogenous ENL, perturbs the recruitment of ENL onto chromatin, and synergizes the BET and DOT1L inhibition-induced downregulation of oncogenes in MLL-rearranged acute leukemia.


    Organizational Affiliation

    Department of Chemistry, The University of Hong Kong, Hong Kong, China. xiangli@hku.hk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein AF-9A, C141Homo sapiensMutation(s): 0 
Gene Names: MLLT3AF9YEATS3
UniProt & NIH Common Fund Data Resources
Find proteins for P42568 (Homo sapiens)
Explore P42568 
Go to UniProtKB:  P42568
PHAROS:  P42568
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide inhibitor PHQ-H3(Q5-K9)B, D7Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.536α = 90
b = 43.992β = 95.86
c = 89.053γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-12-09 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Li, Y., Li, H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91753203
CHINA ASSOCIATION FOR SCIENCE AND TECHNOLOGYChina--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2020-09-16
    Changes: Structure summary