8VLD | pdb_00008vld

Crystal structure of Ash1L PHD finger in complex with histone H3K4me2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation.

Vann, K.R.Sharma, R.Hsu, C.C.Devoucoux, M.Tencer, A.H.Zeng, L.Lin, K.Zhu, L.Li, Q.Lachance, C.Ospina, R.R.Tong, Q.Cheung, K.L.Yang, S.Biswas, S.Xuan, H.Gatchalian, J.Alamillo, L.Wang, J.Jang, S.M.Klein, B.J.Lu, Y.Ernst, P.Strahl, B.D.Rothbart, S.B.Walsh, M.J.Cleary, M.L.Cote, J.Shi, X.Zhou, M.M.Kutateladze, T.G.

(2025) Nat Commun 16: 2235-2235

  • DOI: https://doi.org/10.1038/s41467-025-57556-5
  • Primary Citation of Related Structures:  
    8VLD, 8VLF, 8VLH

  • PubMed Abstract: 

    The histone H3K36-specific methyltransferase ASH1L plays a critical role in development and is frequently dysregulated in human diseases, particularly cancer. Here, we report on the biological functions of the C-terminal region of ASH1L encompassing a bromodomain (ASH1L BD ), a plant homeodomain (ASH1L PHD ) finger, and a bromo-adjacent homology (ASH1L BAH ) domain, structurally characterize these domains, describe their mechanisms of action, and explore functional crosstalk between them. We find that ASH1L PHD recognizes H3K4me2/3, whereas the neighboring ASH1L BD and ASH1L BAH have DNA binding activities. The DNA binding function of ASH1L BAH is a driving force for the association of ASH1L with the linker DNA in the nucleosome, and the large interface with ASH1L PHD stabilizes the ASH1L BAH fold, merging two domains into a single module. We show that ASH1L is involved in embryonic stem cell differentiation and co-localizes with H3K4me3 but not with H3K36me2 at transcription start sites of target genes and genome wide, and that the interaction of ASH1L PHD with H3K4me3 is inhibitory to the H3K36me2-specific catalytic activity of ASH1L. Our findings shed light on the mechanistic details by which the C-terminal domains of ASH1L associate with chromatin and regulate the enzymatic function of ASH1L.


  • Organizational Affiliation
    • Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase ASH1L
A, B
56Homo sapiensMutation(s): 0 
Gene Names: ASH1L
EC: 2.1.1.367 (UniProt), 2.1.1.359 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR48 (Homo sapiens)
Explore Q9NR48 
Go to UniProtKB:  Q9NR48
PHAROS:  Q9NR48
GTEx:  ENSG00000116539 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR48
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3CC [auth T],
D [auth P]
11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NXT2 (Homo sapiens)
Explore Q6NXT2 
Go to UniProtKB:  Q6NXT2
PHAROS:  Q6NXT2
GTEx:  ENSG00000188375 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NXT2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.96α = 90
b = 49.96β = 90
c = 46.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release