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- PDB-7rwp: Crystal Structure of BPTF bromodomain in complex with 5-[4-(amino... -

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Entry
Database: PDB / ID: 7rwp
TitleCrystal Structure of BPTF bromodomain in complex with 5-[4-(aminomethyl)anilino]-4-chloro-2-methylpyridazin-3(2H)-one
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION/INHIBITOR / BRD4 / GENE REGULATION / GENE REGULATION-INHIBITOR complex
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / : / embryonic placenta development / 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 / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / dendrite / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7WZ / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsZahid, H. / Buchholz, C. / Johnson, J.A. / Shi, K. / Aihara, H. / Pomerantz, W.C.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)5T32GM008347-23 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition.
Authors: Zahid, H. / Buchholz, C.R. / Singh, M. / Ciccone, M.F. / Chan, A. / Nithianantham, S. / Shi, K. / Aihara, H. / Fischer, M. / Schonbrunn, E. / Dos Santos, C.O. / Landry, J.W. / Pomerantz, W.C.K.
History
DepositionAug 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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)15,7133
Polymers15,4081
Non-polymers3052
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.131, 66.337, 70.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-3341-

HOH

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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: 15408.423 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 BL21(DE3) (bacteria) / References: UniProt: Q12830
#2: Chemical ChemComp-7WZ / 5-[4-(aminomethyl)anilino]-4-chloro-2-methylpyridazin-3(2H)-one


Mass: 264.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13ClN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.73→48.31 Å / Num. obs: 13678 / % possible obs: 98.7 % / Redundancy: 1.8 % / Biso Wilson estimate: 17.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.7
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.381 / Num. unique obs: 745 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7jt4

7jt4


Resolution: 1.73→48.31 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 658 4.82 %
Rwork0.1753 12999 -
obs0.1768 13657 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.74 Å2 / Biso mean: 21.5953 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 1.73→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 19 199 1182
Biso mean--26.42 31.38 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.860.27391280.238325822710100
1.86-2.050.21841130.19172600271399
2.05-2.350.21651360.17452582271899
2.35-2.960.18951460.17442607275399
2.96-48.310.1981350.15942628276394

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