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- PDB-7dmy: The crystal structure of Cpd7 in complex with BPTF bromodomain -

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Basic information

Entry
Database: PDB / ID: 7dmy
TitleThe crystal structure of Cpd7 in complex with BPTF bromodomain
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsPROTEIN BINDING / inhibitor / BPTF / Bromodomain
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 / chromatin / regulation of DNA-templated transcription / 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 / metal ion binding / nucleus / 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-HAF / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,3672
Polymers16,9271
Non-polymers4401
Water27015
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)75.011, 44.931, 40.838
Angle α, β, γ (deg.)90.000, 95.350, 90.000
Int Tables number5
Space group name H-MC121

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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: 16927.086 Da / Num. of mol.: 1 / Fragment: Bromodomain
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-HAF / tert-butyl 3-methyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]-4-oxidanylidene-5,7-dihydropyrrolo[3,4-d]pyrimidine-6-carboxylate


Mass: 439.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium acetate, 20% PEG 3350, pH 7.1

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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→50 Å / Num. obs: 9269 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.25 Å2 / CC1/2: 0.967 / Net I/σ(I): 9.16
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 9269 / CC1/2: 0.935

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV2

3uv2


Resolution: 2→37.342 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 32.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 493 5.39 %
Rwork0.2525 8653 -
obs0.2545 9146 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.16 Å2 / Biso mean: 34.5363 Å2 / Biso min: 9.21 Å2
Refinement stepCycle: final / Resolution: 2→37.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 65 15 1066
Biso mean--39.02 26.41 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131054
X-RAY DIFFRACTIONf_angle_d1.4491431
X-RAY DIFFRACTIONf_chiral_restr0.057148
X-RAY DIFFRACTIONf_plane_restr0.009181
X-RAY DIFFRACTIONf_dihedral_angle_d15.463636
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.2010.4011150.3115214798
2.201-2.51940.33541450.2872211498
2.5194-3.17390.3323990.2675220299
3.1739-3.420.22291340.216219099

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