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- PDB-6zci: Crystal structure of BRD4-BD1 in complex with NVS-BET-1 -

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Basic information

Entry
Database: PDB / ID: 6zci
TitleCrystal structure of BRD4-BD1 in complex with NVS-BET-1
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / chromatin binding / bromodomain / acetylated histone binding / transcription regulation
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
Chem-QFN / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.976 Å
AuthorsFaller, M.
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: BET bromodomain inhibitors regulate keratinocyte plasticity.
Authors: Schutzius, G. / Kolter, C. / Bergling, S. / Tortelli, F. / Fuchs, F. / Renner, S. / Guagnano, V. / Cotesta, S. / Rueeger, H. / Faller, M. / Bouchez, L. / Salathe, A. / Nigsch, F. / Richards, ...Authors: Schutzius, G. / Kolter, C. / Bergling, S. / Tortelli, F. / Fuchs, F. / Renner, S. / Guagnano, V. / Cotesta, S. / Rueeger, H. / Faller, M. / Bouchez, L. / Salathe, A. / Nigsch, F. / Richards, S.M. / Louis, M. / Gruber, V. / Aebi, A. / Turner, J. / Grandjean, F. / Li, J. / Dimitri, C. / Thomas, J.R. / Schirle, M. / Blank, J. / Drueckes, P. / Vaupel, A. / Tiedt, R. / Manley, P.W. / Klopp, J. / Hemmig, R. / Zink, F. / Leroy, N. / Carbone, W. / Roma, G. / Keller, C.G. / Dales, N. / Beyerbach, A. / Zimmerlin, A. / Bonenfant, D. / Terranova, R. / Berwick, A. / Sahambi, S. / Reynolds, A. / Jennings, L.L. / Ruffner, H. / Tarsa, P. / Bouwmeester, T. / Driver, V. / Frederiksen, M. / Lohmann, F. / Kirkland, S.
History
DepositionJun 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9802
Polymers17,5711
Non-polymers4091
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7080 Å2
Unit cell
Length a, b, c (Å)38.615, 44.058, 80.552
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17571.053 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 BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-QFN / (4~{R})-4-(4-chlorophenyl)-1-cyclopropyl-5-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)-3-methyl-4~{H}-pyrrolo[3,4-c]pyrazol-6-one


Mass: 408.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200 mM Sodium Malonate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.98→38.65 Å / Num. obs: 8489 / % possible obs: 83.62 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03401 / Net I/σ(I): 10.73
Reflection shellResolution: 1.98→2.05 Å / Num. unique obs: 822 / CC1/2: 0.904

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (3-OCT-2019)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.976→40 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.863 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.273 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.208
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 408 -RANDOM
Rwork0.2153 ---
obs0.2179 8490 83.8 %-
Displacement parametersBiso mean: 34.72 Å2
Baniso -1Baniso -2Baniso -3
1--3.4277 Å20 Å20 Å2
2---6.6245 Å20 Å2
3---10.0522 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.976→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 29 104 1127
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071057HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.781455HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d331SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes173HARMONIC5
X-RAY DIFFRACTIONt_it1057HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion140SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact909SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion14.68
LS refinement shellResolution: 1.98→2 Å
RfactorNum. reflection% reflection
Rfree0.4472 21 -
Rwork0.2703 --
obs0.2781 425 99.54 %
Refinement TLS params.Origin x: -11.6128 Å / Origin y: 2.6071 Å / Origin z: -9.4903 Å
111213212223313233
T-0.0492 Å20.034 Å2-0.025 Å2--0.0648 Å2-0.0217 Å2---0.0982 Å2
L2.7308 °2-0.0651 °20.9972 °2-2.317 °2-0.9082 °2--3.6144 °2
S0.0642 Å °-0.0756 Å °-0.1715 Å °-0.0756 Å °-0.1498 Å °-0.001 Å °-0.1715 Å °-0.001 Å °0.0856 Å °
Refinement TLS groupSelection details: { A|* }

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