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- PDB-7lp0: Crystal structure of BPTF bromodomain in complex with inhibitor P... -

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Basic information

Entry
Database: PDB / ID: 7lp0
TitleCrystal structure of BPTF bromodomain in complex with inhibitor Pdy-3-077
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION/INHIBITOR / BPTF / bromodomain / inhibitor / 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-P2L / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
Model detailsCocrystal structure of BPTF bromodomain
AuthorsChan, A. / Schonbrunn, E.
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
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 21, 2024Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6277
Polymers28,9112
Non-polymers7165
Water2,342130
1
A: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7122
Polymers14,4551
Non-polymers2571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9145
Polymers14,4551
Non-polymers4594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.210, 38.570, 57.630
Angle α, β, γ (deg.)97.140, 103.580, 94.250
Int Tables number1
Space group name H-MP1

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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.: 2 / Fragment: BPTF bromodomain (uniprot residues 2917-3037)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12830
#2: Chemical ChemComp-P2L / 4-chlorol-2-methyl-5-[[(3~{R})-1-methylpiperidin-3-yl]amino]pyridazin-3-one


Mass: 256.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17ClN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2019
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.66→38.05 Å / Num. obs: 25204 / % possible obs: 94.7 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.109 / Net I/σ(I): 10.6
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / Num. unique obs: 1843 / CC1/2: 0.672 / Rrim(I) all: 0.652 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 7K6R

7k6r


Resolution: 1.66→38.05 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1200 4.76 %
Rwork0.1906 24000 -
obs0.1928 25200 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.58 Å2 / Biso mean: 27.8499 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 1.66→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 46 130 2040
Biso mean--30.89 31.73 -
Num. residues----226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.66-1.730.41731310.33312615274692
1.73-1.810.32681290.30572593272292
1.81-1.90.34441300.27732599272994
1.9-2.020.30651330.2672664279794
2.02-2.170.24251320.19532646277894
2.18-2.390.23211370.17282724286196
2.39-2.740.22311360.17522737287397
2.74-3.450.21471360.17562719285597
3.45-38.050.19511360.16122703283996
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)
14.8587-3.8367-1.21149.2481.74772.65110.18210.10240.37-0.6308-0.0354-0.2758-0.30640.1747-0.16740.1753-0.03090.00060.18680.00820.185814.286120.7346-8.5116
23.34932.0843-4.14096.5715-2.01296.2607-0.08860.2171-0.42890.15090.07380.34290.473-0.31020.11470.1947-0.03610.00140.1694-0.01480.21527.04441.37690.7713
38.86736.7451-7.12825.2-5.64546.22180.13250.1030.54370.19670.26840.4949-0.5503-0.9489-0.37330.16290.02080.01940.28280.00840.1880.49768.4896.8761
42.4077-3.23833.25774.392-4.42484.4830.13530.1579-0.0885-0.0528-0.10130.30510.16860.147-0.01190.1883-0.0097-0.01350.1855-0.0080.16495.059814.9355-6.4948
56.86131.97692.03126.9077-3.03875.12780.22390.391-0.1262-0.29430.0528-0.15690.1341-0.1099-0.1640.19540.0511-0.00490.1665-0.01370.20924.59523.4104-5.4673
63.6982.871-2.48196.0847-2.23724.4228-0.0161-0.13730.10520.0456-0.0728-0.0896-0.10040.0790.07260.1105-0.0053-0.01660.1632-0.00920.11119.441313.67976.0743
77.20885.2567-4.3267.8374-4.86995.03730.0047-0.2515-0.1950.2058-0.11-0.2409-0.03260.27420.15250.12570.0337-0.03250.1939-0.02610.133218.240110.69483.5591
82.85480.30521.11853.9763-0.34694.6598-0.0479-0.0002-0.1820.20550.1114-0.32030.2780.2151-0.06160.140.00190.01440.19-0.03650.1581.099411.1004-20.2902
96.0559-1.1723.71514.9883-1.62942.8538-0.4134-0.13430.60260.1910.13440.4168-0.2686-0.5490.29790.20330.0378-0.00150.3153-0.0010.2875-12.712423.0117-30.736
101.6161-0.471.15974.9549-5.2188.02730.0632-0.0814-0.0706-0.0167-0.1084-0.00570.1385-0.05220.05990.1015-0.02230.00060.1442-0.01290.1398-6.285711.6405-26.0403
117.5275-5.13874.1914.5275-2.94224.67960.06060.0654-0.0789-0.07190.06730.04050.05350.2136-0.07420.1293-0.05810.03250.2157-0.02590.18014.707217.0492-29.204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2925 through 2945 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2946 through 2963 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2964 through 2973 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2974 through 2982 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 2983 through 2988 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 2989 through 3006 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 3007 through 3035 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 2921 through 2952 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 2953 through 2973 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 2974 through 3006 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 3007 through 3035 )B0

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