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- PDB-7dn4: The crystal structure of Cpd8 in complex with BPTF bromodomain -

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Basic information

Entry
Database: PDB / ID: 7dn4
TitleThe crystal structure of Cpd8 in complex with BPTF bromodomain
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsPROTEIN BINDING / inhibitor / BPTF / bromodomain / reader
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-JC3 / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.841 Å
AuthorsXiong, L. / Guo, Y. / Yang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81930125 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Discovery of selective BPTF bromodomain inhibitors by screening and structure-based optimization.
Authors: Xiong, L. / Mao, X. / Guo, Y. / Zhou, Y. / Chen, M. / Chen, P. / Yang, S. / Li, L.
History
DepositionDec 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Nucleosome-remodeling factor subunit BPTF
B: Nucleosome-remodeling factor subunit BPTF
C: Nucleosome-remodeling factor subunit BPTF
D: Nucleosome-remodeling factor subunit BPTF
E: Nucleosome-remodeling factor subunit BPTF
F: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,76312
Polymers86,7326
Non-polymers2,0316
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.751, 166.751, 161.484
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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: 14455.415 Da / Num. of mol.: 6 / Fragment: Bromodoamin and PHD finger
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-JC3 / 3-methyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-one


Mass: 338.447 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H26N4O / Feature type: SUBJECT OF INVESTIGATION
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: 3.74 Å3/Da / Density % sol: 67.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2 M Ammonium sulfate, 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate, pH5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97875 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 2.841→144.411 Å / Num. obs: 31789 / % possible obs: 99.9 % / Redundancy: 39.2 % / Biso Wilson estimate: 70.11 Å2 / CC1/2: 0.987 / Net I/σ(I): 8.2
Reflection shellResolution: 2.841→2.89 Å / Num. unique obs: 31789 / CC1/2: 0.9877

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV2

3uv2


Resolution: 2.841→53.823 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3461 1627 5.19 %
Rwork0.2668 29736 -
obs0.271 31363 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.82 Å2 / Biso mean: 82.3194 Å2 / Biso min: 27.91 Å2
Refinement stepCycle: final / Resolution: 2.841→53.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 306 0 6150
Biso mean--70.42 --
Num. residues----708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166279
X-RAY DIFFRACTIONf_angle_d1.5188515
X-RAY DIFFRACTIONf_chiral_restr0.064900
X-RAY DIFFRACTIONf_plane_restr0.0121072
X-RAY DIFFRACTIONf_dihedral_angle_d18.4443837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.841-2.92420.47921290.3968248099
2.9242-3.01860.38831180.34492444100
3.0186-3.12650.42131410.34072443100
3.1265-3.25160.32721320.30482461100
3.2516-3.39960.37211510.29912476100
3.3996-3.57880.43081140.2882480100
3.5788-3.8030.37211380.26882497100
3.803-4.09650.38441490.2537245799
4.0965-4.50860.32421390.22642511100
4.5086-5.16050.28081390.2287250799
5.1605-6.49990.29111300.2504254599
6.4999-53.8230.32441470.2467243590

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