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- PDB-9m0f: The crystal structure of BRD4-BDs in complex with H2A peptide -

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Basic information

Entry
Database: PDB / ID: 9m0f
TitleThe crystal structure of BRD4-BDs in complex with H2A peptide
Components
  • (Bromodomain-containing protein 4) x 2
  • Histone H2A
KeywordsPROTEIN BINDING / Bromodomain / Acetylation
Function / homology
Function and homology information


histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / 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 / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsWang, X.D. / Ji, J.H. / Yang, H.W. / Li, Z.B. / Yang, N.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170549 China
National Natural Science Foundation of China (NSFC)32370731 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural mechanism of diacetylated histone H2A recognition by Bromodomain-containing protein 4 in Regulation of non-homologous end-joining DNA repair.
Authors: Wang, X. / Ji, J. / Ma, Y. / Liu, L. / Bao, K. / Yang, H. / Li, Z. / Li, T. / Shi, L. / Yang, N.
History
DepositionFeb 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
E: Histone H2A
F: Histone H2A


Theoretical massNumber of molelcules
Total (without water)54,6936
Polymers54,6936
Non-polymers00
Water1,42379
1
A: Bromodomain-containing protein 4
E: Histone H2A

C: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)27,3473
Polymers27,3473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
2
B: Bromodomain-containing protein 4
F: Histone H2A

D: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)27,3473
Polymers27,3473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Unit cell
Length a, b, c (Å)125.453, 70.446, 92.958
Angle α, β, γ (deg.)90.000, 126.967, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 13850.028 Da / Num. of mol.: 2
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
#2: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 12537.589 Da / Num. of mol.: 2
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
#3: Protein/peptide Histone H2A


Mass: 959.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, Sodium citrate tribasic dihydrate, 1-propanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.61→74.27 Å / Num. obs: 19865 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.995 / Net I/σ(I): 8.3
Reflection shellResolution: 2.61→2.66 Å / Num. unique obs: 6587 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→74.27 Å / SU ML: 0.3424 / Cross valid method: THROUGHOUT / Phase error: 26.7243 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2544 1982 9.99 %
Rwork0.2077 17857 -
obs0.2124 19838 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.4 Å2
Refinement stepCycle: LAST / Resolution: 2.61→74.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 0 79 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533742
X-RAY DIFFRACTIONf_angle_d1.16695045
X-RAY DIFFRACTIONf_chiral_restr0.0639524
X-RAY DIFFRACTIONf_plane_restr0.0042647
X-RAY DIFFRACTIONf_dihedral_angle_d6.47732263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.680.29621430.2791283X-RAY DIFFRACTION99.58
2.68-2.750.30251390.2551255X-RAY DIFFRACTION99.93
2.75-2.830.32321400.24981270X-RAY DIFFRACTION99.79
2.83-2.920.28811390.24391251X-RAY DIFFRACTION99.93
2.92-3.020.30181400.24241254X-RAY DIFFRACTION99.5
3.02-3.150.34071440.24181288X-RAY DIFFRACTION99.79
3.15-3.290.29471400.24121263X-RAY DIFFRACTION100
3.29-3.460.30461400.22831262X-RAY DIFFRACTION100
3.46-3.680.24581420.20541271X-RAY DIFFRACTION100
3.68-3.960.22171420.19471288X-RAY DIFFRACTION100
3.96-4.360.23261430.15941280X-RAY DIFFRACTION100
4.36-4.990.20091420.17141274X-RAY DIFFRACTION100
4.99-6.290.25141440.20071303X-RAY DIFFRACTION100
6.29-74.270.21141440.19381315X-RAY DIFFRACTION98.92

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