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

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Basic information

Entry
Database: PDB / ID: 7rwq
TitleCrystal Structure of BPTF bromodomain in complex with 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-6-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 / 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-7XE / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)15,7393
Polymers15,4081
Non-polymers3312
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.180, 66.346, 71.216
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-3227-

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-7XE / 4-chloro-2-methyl-5-[(1,2,3,4-tetrahydroisoquinolin-6-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-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.: 166 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
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: 1.9→71.22 Å / Num. obs: 10748 / % possible obs: 99.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.074 / Rrim(I) all: 0.105 / Net I/σ(I): 9.3 / Num. measured all: 19653
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
1.9-1.941.90.35612996950.6420.3560.5042100
9.09-71.221.40.0191821290.9990.0190.02623.799.4

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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: 1.9→48.54 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 496 4.63 %
Rwork0.1985 10215 -
obs0.1996 10711 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.08 Å2 / Biso mean: 21.7955 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: final / Resolution: 1.9→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 21 166 1164
Biso mean--20.88 29.17 -
Num. residues----118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.090.31791310.266724982629100
2.09-2.390.23111080.22322517262599
2.39-3.010.18561040.188325762680100
3.01-48.540.20661530.17752624277799
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)
12.33931.51881.15996.38481.21151.6869-0.15590.3958-0.0987-0.67750.1712-0.0947-0.01670.2601-0.04240.1950.01310.02150.19840.03190.19020.8889-23.059810.1537
28.0353-2.45722.11533.1266-0.80743.3782-0.25-0.29390.48160.19960.14490.0076-0.3373-0.26270.13630.1859-0.00480.00880.1202-0.02890.1748-6.4382-0.943416.5539
32.0607-1.70310.96163.9384-0.42740.89810.1033-0.1071-0.159-0.04820.16110.49450.0854-0.2719-0.13220.1554-0.0122-0.00510.19020.01720.1465-10.9505-9.758611.062
44.6334-1.1864-0.69136.1652-2.99994.02650.11990.3022-0.4229-0.06510.13150.5170.2813-0.3858-0.07380.1757-0.0324-0.03240.15980.01760.1955-8.9792-23.02528.61
51.9681-1.03180.13872.33810.15131.32720.0348-0.02740.0157-0.12750.0245-0.1662-0.00490.1237-0.0560.1208-0.00930.01770.15050.01760.13241.2245-8.47677.4319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2794 through 2818 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2819 through 2837 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2838 through 2856 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2857 through 2862 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 2863 through 2911 )A0

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