8SB6

Structure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Acetyl-methyllysine marks chromatin at active transcription start sites.

Lu-Culligan, W.J.Connor, L.J.Xie, Y.Ekundayo, B.E.Rose, B.T.Machyna, M.Pintado-Urbanc, A.P.Zimmer, J.T.Vock, I.W.Bhanu, N.V.King, M.C.Garcia, B.A.Bleichert, F.Simon, M.D.

(2023) Nature 622: 173-179

  • DOI: https://doi.org/10.1038/s41586-023-06565-9
  • Primary Citation of Related Structures:  
    8SB6

  • PubMed Abstract: 

    Lysine residues in histones and other proteins can be modified by post-translational modifications that encode regulatory information 1 . Lysine acetylation and methylation are especially important for regulating chromatin and gene expression 2-4 . Pathways involving these post-translational modifications are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. Here we report cellular lysine residues that are both methylated and acetylated on the same side chain to form N ε -acetyl-N ε -methyllysine (Kacme). We show that Kacme is found on histone H4 (H4Kacme) across a range of species and across mammalian tissues. Kacme is associated with marks of active chromatin, increased transcriptional initiation and is regulated in response to biological signals. H4Kacme can be installed by enzymatic acetylation of monomethyllysine peptides and is resistant to deacetylation by some HDACs in vitro. Kacme can be bound by chromatin proteins that recognize modified lysine residues, as we demonstrate with the crystal structure of acetyllysine-binding protein BRD2 bound to a histone H4Kacme peptide. These results establish Kacme as a cellular post-translational modification with the potential to encode information distinct from methylation and acetylation alone and demonstrate that Kacme has all the hallmarks of a post-translational modification with fundamental importance to chromatin biology.


  • Organizational Affiliation

    Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain containing 2
A, B, C
124Homo sapiensMutation(s): 0 
Gene Names: BRD2
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
D, E
15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
7QK
Query on 7QK
D, E
L-PEPTIDE LINKINGC9 H18 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.378α = 90
b = 55.819β = 94.414
c = 68.006γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM137117
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM141313

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Database references
  • Version 1.4: 2023-11-15
    Changes: Data collection, Derived calculations