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- PDB-36iv: Cryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes -

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Basic information

Entry
Database: PDB / ID: 36iv
TitleCryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes
Components
  • DNA (130-MER)
  • DNA (132-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3
  • Histone H4
  • Isoform C of Bromodomain-containing protein 4
KeywordsNUCLEAR PROTEIN/DNA / Chromatin 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 / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / condensed nuclear chromosome / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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 / Metalloprotease DUBs / RMTs methylate histone arginines / innate immune response in mucosa / HCMV Early Events / p53 binding / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / UCH proteinases / nucleosome assembly / chromosome / E3 ubiquitin ligases ubiquitinate target proteins / HATs acetylate histones / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Dengue Virus-Host Interactions / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / histone binding / antibacterial humoral response / Oxidative Stress Induced Senescence / chromatin organization / Estrogen-dependent gene expression / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Bromodomain-containing protein 4 / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhu, J. / Leith, E.M. / O'Donnell, E.N. / Manzano, B.P. / Wu, S.-Y. / Chiang, C.-M. / Armache, J.-P. / Tan, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127034 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes
Authors: Zhu, J. / Leith, E.M. / Tan, S.
History
DepositionJun 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (132-MER)
J: DNA (130-MER)
K: Isoform C of Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)291,55111
Polymers291,55111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, Crosslinked by GraFix and examined the complex on Native PAGE
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3


Mass: 15344.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4


Mass: 11402.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14034.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13804.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#7: Protein Isoform C of Bromodomain-containing protein 4 / Protein HUNK1


Mass: 80506.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (132-MER)


Mass: 50683.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (130-MER)


Mass: 51190.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BRD4 bound to acetylated nucleosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.378 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer componentConc.: 20 mM / Name: potassium chloride / Formula: KCl
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Monodisperse particles were observed in the majority of the collected movies.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80704 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413120
ELECTRON MICROSCOPYf_angle_d0.73818812
ELECTRON MICROSCOPYf_dihedral_angle_d31.7843570
ELECTRON MICROSCOPYf_chiral_restr0.0432130
ELECTRON MICROSCOPYf_plane_restr0.0061505

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