36IV | pdb_000036iv

Cryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

BRD4 binds the nucleosome via both histone and DNA interactions.

Zhu, J.Leith, E.M.O'Donnell, E.N.Manzano, B.P.Wu, S.Y.Chiang, C.M.Armache, J.P.Tan, S.

(2026) Mol Cell 86: 3185-3197.e7

  • DOI: https://doi.org/10.1016/j.molcel.2026.07.012
  • Primary Citation Related Structures: 
    36IU, 36IV

  • PubMed Abstract: 

    BRD4, a bromodomain and extraterminal (BET) family transcriptional regulator, is believed to be recruited to chromatin via interactions between its tandem bromodomains (BD1 and BD2) and acetylated histone tails. Although extensive studies have explained how individual BRD4 bromodomains bind to acetylated peptides and how BET inhibitors interfere with such interactions, equivalent studies of the full-length BRD4 protein with the nucleosome have been lacking. Our cryo-electron microscopy (cryo-EM) structure of the BRD4 short (BRD4-S) isoform bound to a nucleosome diacetylated on histone H4 shows how BRD4 BD1 engages both the H4 tail and nucleosomal DNA. Unlike other chromatin reader domain/nucleosome structures, BRD4 BD1 presents the acetylated histone tail for potential interactions with additional chromatin proteins. Unexpectedly, our biochemical studies indicate that BRD4 uses basic regions outside of the bromodomains to bind nucleosomes tightly even in the absence of histone acetylation. Our results further show that histone H4 acetylation influences the conformation of the BRD4/nucleosome complex.


  • Organizational Affiliation
    • Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

Macromolecule Content 

  • Total Structure Weight: 291.55 kDa 
  • Atom Count: 12,375 
  • Modeled Residue Count: 1,150 
  • Deposited Residue Count: 2,036 
  • Unique protein chains: 5
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3
A, E
135Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065LOC108703785LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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Go to UniProtKB:  A0A310TTQ1
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UniProt GroupA0A310TTQ1
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
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UniProt GroupP62799
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
129Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
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UniProt GroupP04908
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
125Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform C of Bromodomain-containing protein 4722Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
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Find proteins for O60885 (Homo sapiens)
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PHAROS:  O60885
GTEx:  ENSG00000141867 
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UniProt GroupO60885
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (132-MER)165synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (130-MER)165synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A, E
L-PEPTIDE LINKINGC8 H16 N2 O3LYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127034

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Data collection, Database references