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- PDB-8ag2: Crystal structure of the BPTF bromodomain in complex with BI-7190 -

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Basic information

Entry
Database: PDB / ID: 8ag2
TitleCrystal structure of the BPTF bromodomain in complex with BI-7190
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsPROTEIN BINDING / Bromodomain / Inhibitor / Complex
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-M1I / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.025 Å
AuthorsBader, G. / Boettcher, J. / Wolkerstorfer, B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: Chemmedchem / Year: 2023
Title: Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments.
Authors: Martinelli, P. / Schaaf, O. / Mantoulidis, A. / Martin, L.J. / Fuchs, J.E. / Bader, G. / Gollner, A. / Wolkerstorfer, B. / Rogers, C. / Balikci, E. / Lipp, J.J. / Mischerikow, N. / Doebel, S. ...Authors: Martinelli, P. / Schaaf, O. / Mantoulidis, A. / Martin, L.J. / Fuchs, J.E. / Bader, G. / Gollner, A. / Wolkerstorfer, B. / Rogers, C. / Balikci, E. / Lipp, J.J. / Mischerikow, N. / Doebel, S. / Gerstberger, T. / Sommergruber, W. / Huber, K.V.M. / Bottcher, J.
History
DepositionJul 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 22, 2023Group: 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 1.3Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6192
Polymers14,2371
Non-polymers3821
Water4,324240
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 area7290 Å2
Unit cell
Length a, b, c (Å)27.241, 65.791, 39.728
Angle α, β, γ (deg.)90, 102.51, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleosome-remodeling factor subunit BPTF / Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal ...Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal Alzheimer antigen


Mass: 14237.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q12830
#2: Chemical ChemComp-M1I / 5-[3-methoxy-4-[1-(4-methylpiperazin-1-yl)cyclopropyl]phenyl]-1,3,4-trimethyl-pyridin-2-one


Mass: 381.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H31N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32 % PEG1 000 200 mM magnesium chloride 100 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000021 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000021 Å / Relative weight: 1
ReflectionResolution: 1.025→38.784 Å / Num. obs: 54717 / % possible obs: 79.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 11.1
Reflection shellResolution: 1.025→1.091 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2737 / Rsym value: 0.569 / % possible all: 23.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
autoPROCdata reduction
XDSJan 26, 201data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV2

3uv2


Resolution: 1.025→38.78 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU R Cruickshank DPI: 0.029 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.03 / SU Rfree Blow DPI: 0.031 / SU Rfree Cruickshank DPI: 0.029
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2673 -RANDOM
Rwork0.1546 ---
obs0.1554 54717 80 %-
Displacement parametersBiso mean: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.1206 Å20 Å2-0.0494 Å2
2--0.2269 Å20 Å2
3----0.1063 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.025→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 28 240 1268
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012109HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.943811HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d624SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes322HARMONIC5
X-RAY DIFFRACTIONt_it2078HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion130SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2098SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion12.6
LS refinement shellResolution: 1.03→1.06 Å
RfactorNum. reflection% reflection
Rfree0.2773 56 -
Rwork0.2418 --
obs--16.22 %

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