7M5U

Crystal structure of human MPP8 chromodomain in complex with peptidomimetic ligand UNC5246


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A Peptidomimetic Ligand Targeting the Chromodomain of MPP8 Reveals HRP2's Association with the HUSH Complex.

Waybright, J.M.Clinkscales, S.E.Barnash, K.D.Budziszewski, G.R.Rectenwald, J.M.Chiarella, A.M.Norris-Drouin, J.L.Cholensky, S.H.Pearce, K.H.Herring, L.E.McGinty, R.K.Hathaway, N.A.James, L.I.

(2021) ACS Chem Biol 16: 1721-1736

  • DOI: https://doi.org/10.1021/acschembio.1c00429
  • Primary Citation of Related Structures:  
    7M5U

  • PubMed Abstract: 

    The interpretation of histone post-translational modifications (PTMs), specifically lysine methylation, by specific classes of "reader" proteins marks an important aspect of epigenetic control of gene expression. Methyl-lysine (Kme) readers often regulate gene expression patterns through the recognition of a specific Kme PTM while participating in or recruiting large protein complexes that contain enzymatic or chromatin remodeling activity. Understanding the composition of these Kme-reader-containing protein complexes can serve to further our understanding of the biological roles of Kme readers, while small molecule chemical tools can be valuable reagents in interrogating novel protein-protein interactions. Here, we describe our efforts to target the chromodomain of M-phase phosphoprotein 8 (MPP8), a member of the human silencing hub (HUSH) complex and a histone 3 lysine 9 trimethyl (H3K9me3) reader that is vital for heterochromatin formation and has specific roles in cancer metastasis. Utilizing a one-bead, one-compound (OBOC) combinatorial screening approach, we identified UNC5246, a peptidomimetic ligand capable of interacting with the MPP8 chromodomain in the context of the HUSH complex. Additionally, a biotinylated derivative of UNC5246 facilitated chemoproteomics studies which revealed hepatoma-derived growth factor-related protein 2 (HRP2) as a novel protein associated with MPP8. HRP2 was further shown to colocalize with MPP8 at the E-cadherin gene locus, suggesting a possible role in cancer cell plasticity.


  • Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M-phase phosphoprotein 862Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH8MPP8
UniProt & NIH Common Fund Data Resources
Find proteins for Q99549 (Homo sapiens)
Explore Q99549 
Go to UniProtKB:  Q99549
PHAROS:  Q99549
GTEx:  ENSG00000196199 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99549
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UNC52467Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
5T3
Query on 5T3
B
L-PEPTIDE LINKINGC11 H24 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.123α = 90
b = 87.123β = 90
c = 57.802γ = 120
Software Package:
Software NamePurpose
XDSdata processing
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR61DA047023
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133498

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection