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- PDB-8b5c: Human BRD4 bromdomain 1 in complex with a H4 peptide containing A... -

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Basic information

Entry
Database: PDB / ID: 8b5c
TitleHuman BRD4 bromdomain 1 in complex with a H4 peptide containing ApmTri (H4K5/8ApmTri)
Components
  • Bromodomain-containing protein 4
  • H4K5/8ApmTri
KeywordsPEPTIDE BINDING PROTEIN / ApmTri / acetyl-lysine mimic / BET-Bromodomain / histone-peptide
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / 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: 1.58 Å
AuthorsBraun, M.B. / Bartlick, N. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW 1163/9-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family.
Authors: Kirchgassner, S. / Braun, M.B. / Bartlick, N. / Koc, C. / Reinkemeier, C.D. / Lemke, E.A. / Stehle, T. / Schwarzer, D.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0May 24, 2023Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: H4K5/8ApmTri


Theoretical massNumber of molelcules
Total (without water)16,5562
Polymers16,5562
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, MST
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-8 kcal/mol
Surface area7410 Å2
Unit cell
Length a, b, c (Å)42.527, 46.748, 58.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 15294.578 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
#2: Protein/peptide H4K5/8ApmTri


Mass: 1261.441 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: non-natural amino acid ApmTri containing H4 peptide
Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.82 Å3/Da / Density % sol: 32.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM sodium acetate trihydrate 100 mM Trishydrochloride pH 8.5 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999867 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999867 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 16702 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.71 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.47
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 2628 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.58→36.62 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 1503 9 %
Rwork0.1842 15195 -
obs0.1863 16698 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.57 Å2
Refinement stepCycle: LAST / Resolution: 1.58→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 78 1171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661130
X-RAY DIFFRACTIONf_angle_d0.89821538
X-RAY DIFFRACTIONf_chiral_restr0.0468164
X-RAY DIFFRACTIONf_plane_restr0.0064196
X-RAY DIFFRACTIONf_dihedral_angle_d2.9296941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.630.32871320.30591338X-RAY DIFFRACTION99.66
1.63-1.690.31191330.26471349X-RAY DIFFRACTION99.66
1.69-1.750.29261350.26951364X-RAY DIFFRACTION99.67
1.75-1.830.2981350.21591357X-RAY DIFFRACTION99.73
1.83-1.930.21911350.19021368X-RAY DIFFRACTION99.93
1.93-2.050.19231350.17971365X-RAY DIFFRACTION100
2.05-2.210.21071370.16611381X-RAY DIFFRACTION100
2.21-2.430.19021360.16711376X-RAY DIFFRACTION99.6
2.43-2.780.21261380.1781399X-RAY DIFFRACTION99.81
2.78-3.510.18881390.17071402X-RAY DIFFRACTION99.94
3.51-36.620.17521480.16911496X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: -7.52012485661 Å / Origin y: 7.80694949755 Å / Origin z: -16.6646782266 Å
111213212223313233
T0.149215471378 Å2-0.00197945846376 Å2-0.00920603783542 Å2-0.150352982571 Å20.0147625369133 Å2--0.148517949834 Å2
L0.160063559515 °20.149349319198 °20.0119025861183 °2-0.247604837798 °20.00586058025533 °2--0.140235867974 °2
S0.00941259161442 Å °-0.0445250033563 Å °-0.0808033985035 Å °0.0287537446353 Å °-0.0196014680219 Å °-1.1704145578E-5 Å °0.00226584658222 Å °0.00289511082983 Å °3.69710230686E-6 Å °
Refinement TLS groupSelection details: all

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