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- PDB-7rwo: Crystal Structure of BPTF bromodomain in complex with 4-chloro-2-... -

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Basic information

Entry
Database: PDB / ID: 7rwo
TitleCrystal Structure of BPTF bromodomain in complex with 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyridazin-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-7WN / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 2.0Oct 19, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / struct
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 / _entity.pdbx_number_of_molecules / _struct.title
Revision 2.1Oct 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)15,8234
Polymers15,4081
Non-polymers4153
Water3,873215
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)27.098, 66.638, 39.288
Angle α, β, γ (deg.)90.000, 106.790, 90.000
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: 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-7WN / 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyridazin-3(2H)-one


Mass: 290.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15ClN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) polyethylene glycol 1500 and 10% (w/v) proprionate-cacodylate-bis tris propane

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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: 1.58→66.64 Å / Num. obs: 17759 / % possible obs: 96.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 13.65 Å2 / CC1/2: 0.921 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Rrim(I) all: 0.109 / Net I/σ(I): 9.4 / Num. measured all: 33460
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.58-1.6120.42116918670.6360.4210.595298.2
8.65-66.641.80.0142101200.9990.0140.0228.197.7

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JT4

7jt4


Resolution: 1.58→37.61 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 858 4.85 %
Rwork0.164 16849 -
obs0.166 17707 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.33 Å2 / Biso mean: 19.9483 Å2 / Biso min: 7.83 Å2
Refinement stepCycle: final / Resolution: 1.58→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 28 218 1229
Biso mean--24.54 29.47 -
Num. residues----119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.680.26711510.2052840299198
1.68-1.810.2421500.21232814296498
1.81-1.990.29071290.19342779290895
1.99-2.280.20081700.16372747291796
2.28-2.870.19261220.15882867298998
2.87-37.610.17341360.14052802293895
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5784-0.8026-1.09242.49891.77692.64310.03-0.06250.08630.06510.0946-0.1089-0.01420.1715-0.1030.10680.0027-0.00110.11180.00390.116714.440622.78188.1233
25.67731.4931-2.22382.5779-1.11273.0236-0.10130.1357-0.1389-0.05480.09240.08940.1054-0.19710.00330.0937-0.0014-0.0140.0770.00290.08834.79732.14284.3218
30.89190.5269-0.32436.1809-0.16971.10660.0294-0.02010.06710.05250.03630.10820.0171-0.0239-0.06750.0577-0.00530.00150.10150.00160.07027.790311.37359.2399
42.74180.62050.15225.47760.89792.52330.0595-0.03150.01440.1148-0.0012-0.5202-0.05420.0631-0.05080.0340.02030.00040.09890.00260.073919.554311.59288.557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2793 through 2818 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2819 through 2847 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2848 through 2885 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2886 through 2911 )A0

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