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- EMDB-77606: Cryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes -

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Entry
Database: EMDB / ID: EMD-77606
TitleCryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes
Map datastructure of BRD4 BDI bound to acetylated nucleosomes
Sample
  • Complex: BRD4 bound to acetylated nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (132-MER)
    • DNA: DNA (130-MER)
    • Protein or peptide: Isoform C of Bromodomain-containing protein 4
KeywordsChromatin reader BRD4 Acetylated nucleosome / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone H3K9ac reader activity / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription ...histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone H3K9ac reader activity / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / RNA polymerase II CTD heptapeptide repeat kinase activity / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / condensed nuclear chromosome / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / positive regulation of transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription coregulator activity / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / RMTs methylate histone arginines / HCMV Early Events / Metalloprotease DUBs / innate immune response in mucosa / p53 binding / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / nucleosome assembly / UCH proteinases / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of inflammatory response / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / killing of cells of another organism / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Dengue Virus-Host Interactions / Processing of DNA double-strand break ends / antimicrobial humoral immune response mediated by antimicrobial peptide / Senescence-Associated Secretory Phenotype (SASP) / heterochromatin formation / histone binding / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / defense response to Gram-positive bacterium / transcription cis-regulatory region binding / Ub-specific processing proteases / chromatin remodeling / chromosome / negative regulation of cell population proliferation / protein heterodimerization activity / Amyloid fiber formation / protein serine/threonine kinase activity / chromatin binding
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / : ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Bromodomain, conserved site / Bromodomain signature. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold
Similarity search - Domain/homology
Histone H3 / Bromodomain-containing protein 4 / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhu J / Leith EM / O'Donnell EN / Manzano BP / Wu S-Y / Chiang C-M / Armache J-P / Tan S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127034 United States
CitationJournal: Mol Cell / Year: 2026
Title: BRD4 binds the nucleosome via both histone and DNA interactions.
Authors: Jiang Zhu / Erik M Leith / Erin N O'Donnell / Bryan P Manzano / Shwu-Yuan Wu / Cheng-Ming Chiang / Jean-Paul Armache / Song Tan /
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 ...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.
History
DepositionJun 12, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77606.png

Downloads & links

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Map

FileDownload / File: emd_77606.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of BRD4 BDI bound to acetylated nucleosomes
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 256 pix.
= 259.2 Å		1.01 Å/pix.
x 256 pix.
= 259.2 Å		1.01 Å/pix.
x 256 pix.
= 259.2 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.20935082 - 0.7252547
Average (Standard dev.)0.0051916195 (±0.027895734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77606_msk_1.map
Projections & Slices
AxesZYX

Projections

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Histogram (log scale)

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Mask #2

Fileemd_77606_msk_2.map
Projections & Slices
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Half map: Half Map B

Fileemd_77606_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_77606_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : BRD4 bound to acetylated nucleosome

EntireName: BRD4 bound to acetylated nucleosome
Components
  • Complex: BRD4 bound to acetylated nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (132-MER)
    • DNA: DNA (130-MER)
    • Protein or peptide: Isoform C of Bromodomain-containing protein 4

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Supramolecule #1: BRD4 bound to acetylated nucleosome

SupramoleculeName: BRD4 bound to acetylated nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 378 KDa

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.344959 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPR(ALY)QL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.40234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSGRGKGGKG LG(ALY)GGA(ALY)RHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VT YTEHAKR KTVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.034355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.804045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: Isoform C of Bromodomain-containing protein 4

MacromoleculeName: Isoform C of Bromodomain-containing protein 4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.506195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSAESGPGTR LRNLPVMGDG LETSQMSTTQ AQAQPQPANA ASTNPPPPET SNPNKPKRQT NQLQYLLRVV LKTLWKHQFA WPFQQPVDA VKLNLPDYYK IIKTPMDMGT IKKRLENNYY WNAQECIQDF NTMFTNCYIY NKPGDDIVLM AEALEKLFLQ K INELPTEE ...String:
GSAESGPGTR LRNLPVMGDG LETSQMSTTQ AQAQPQPANA ASTNPPPPET SNPNKPKRQT NQLQYLLRVV LKTLWKHQFA WPFQQPVDA VKLNLPDYYK IIKTPMDMGT IKKRLENNYY WNAQECIQDF NTMFTNCYIY NKPGDDIVLM AEALEKLFLQ K INELPTEE TEIMIVQAKG RGRGRKETGT AKPGVSTVPN TTQASTPPQT QTPQPNPPPV QATPHPFPAV TPDLIVQTPV MT VVPPQPL QTPPPVPPQP QPPPAPAPQP VQSHPPIIAA TPQPVKTKKG VKRKADTTTP TTIDPIHEPP SLPPEPKTTK LGQ RRESSR PVKPPKKDVP DSQQHPAPEK SSKVSEQLKC CSGILKEMFA KKHAAYAWPF YKPVDVEALG LHDYCDIIKH PMDM STIKS KLEAREYRDA QEFGADVRLM FSNCYKYNPP DHEVVAMARK LQDVFEMRFA KMPDEPEEPV VAVSSPAVPP PTKVV APPS SSDSSSDSSS DSDSSTDDSE EERAQRLAEL QEQLKAVHEQ LAALSQPQQN KPKKKEKDKK EKKKEKHKRK EEVEEN KKS KAKEPPPKKT KKNNSSNSNV SKKEPAPMKS KPPPTYESEE EDKCKPMSYE EKRQLSLDIN KLPGEKLGRV VHIIQSR EP SLKNSNPDEI EIDFETLKPS TLRELERYVT SCLRKKRKPQ AEKVDVIAGS SKMKGFSSSE SESSSESSSS DSEDSETG P A

UniProtKB: Bromodomain-containing protein 4

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Macromolecule #5: DNA (132-MER)

MacromoleculeName: DNA (132-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 50.683266 KDa
SequenceString: (DA)(DT)(DC)(DG)(DC)(DC)(DG)(DC)(DC)(DC) (DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT) (DT)(DG)(DG)(DT)(DC)(DG) ...String:
(DA)(DT)(DC)(DG)(DC)(DC)(DG)(DC)(DC)(DC) (DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC) (DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA) (DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC) (DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC)(DC) (DT)(DG)(DT)(DG)(DC)(DA)(DT) (DG)(DT) (DG)(DA)(DT)

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Macromolecule #6: DNA (130-MER)

MacromoleculeName: DNA (130-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.190605 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA) (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA) (DG)(DA)(DC)(DT)(DA)(DG) ...String:
(DA)(DT)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA) (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA) (DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT) (DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA) (DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA) (DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC) (DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DG)(DG)(DC)(DG) (DG)(DC) (DG)(DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5 / Component - Concentration: 20.0 mM / Component - Formula: KCl / Component - Name: potassium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse particles were observed in the majority of the collected movies.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3lz0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80704
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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