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- PDB-7m2e: Crystal structure of BPTF bromodomain in complex with CB02-092 -

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Basic information

Entry
Database: PDB / ID: 7m2e
TitleCrystal structure of BPTF bromodomain in complex with CB02-092
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION / BPTF / Bromodomain / Bromodomain inhibitor
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-YOV / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsNithianantham, S. / Fischer, M.
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
DepositionMar 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 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

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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)14,7622
Polymers14,4551
Non-polymers3071
Water2,954164
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)27.006, 66.546, 39.623
Angle α, β, γ (deg.)90.000, 105.610, 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: 14455.415 Da / Num. of mol.: 1 / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12830
#2: Chemical ChemComp-YOV / 4-chloro-5-{4-[2-(dimethylamino)ethyl]anilino}-2-methylpyridazin-3(2H)-one


Mass: 306.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19ClN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.37 Å3/Da / Density % sol: 48.15 % / Description: Thin needles
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0. 2M NaCl and 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 12469 / % possible obs: 91.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.1 Å2 / CC1/2: 0.959 / CC star: 0.99 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.086 / Rrim(I) all: 0.172 / Χ2: 0.842 / Net I/av σ(I): 9.6 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.782.90.3325380.8550.220.4010.71178.3
1.78-1.812.90.3265480.8370.2170.3940.74881.2
1.81-1.853.10.3075420.8650.1970.3680.72682.1
1.85-1.893.10.2995660.8920.1880.3550.81182.6
1.89-1.933.20.2835470.8570.1770.3360.78380.9
1.93-1.973.10.2755460.8530.1760.3290.87679.9
1.97-2.023.50.266000.9080.1580.3060.91892.3
2.02-2.073.50.2466540.8950.1510.290.93690.7
2.07-2.143.50.2036060.9140.1250.240.89293.1
2.14-2.23.60.2036490.9170.1240.2390.85994.3
2.2-2.283.60.2096500.9040.1280.2470.91495.3
2.28-2.383.70.1986340.9050.1190.2320.8495.3
2.38-2.483.80.2166720.8810.1320.2550.8697.1
2.48-2.6140.2156510.9090.1260.2510.87197.2
2.61-2.783.80.1816550.8940.110.2140.82495.2
2.78-2.994.60.1796870.9510.0980.2050.92499.6
2.99-3.294.80.1436630.9740.0760.1630.81698.8
3.29-3.774.80.1066850.9830.0570.1210.90399.7
3.77-4.754.60.0756830.990.040.0850.75498.6
4.75-504.50.0646930.9950.0350.0730.76898

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.18phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UV2

3uv2


Resolution: 1.75→33.27 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 601 4.88 %
Rwork0.1673 11717 -
obs0.1697 12318 90.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.87 Å2 / Biso mean: 23.4239 Å2 / Biso min: 11.59 Å2
Refinement stepCycle: final / Resolution: 1.75→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 21 165 1171
Biso mean--26.41 31.31 -
Num. residues----120
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 (%)
1.75-1.930.25391130.17982545265878
1.93-2.210.2891420.16212891303389
2.21-2.780.22611660.17943061322795
2.78-33.270.1911800.16173220340099
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)
10.6161-0.4478-0.93241.9310.74411.4896-0.0204-0.06110.1460.05650.1312-0.20380.01590.2681-0.09290.1751-0.007-0.01590.1804-0.01130.179115.18222.8328.45
21.8940.3205-0.74651.0397-0.20271.7515-0.11220.1265-0.18860.00980.04750.08440.1687-0.17960.05150.1802-0.01090.0160.158-0.00870.20224.7042.1574.223
31.8870.3810.02393.35070.31591.19030.02660.08140.1793-0.0204-0.05630.3547-0.0073-0.2840.01890.1263-0.003-0.01340.18750.01650.18054.60419.5255.657
40.54670.3803-0.01692.3907-0.03550.4315-0.0506-0.04260.00220.1080.20410.03660.06220.0624-0.11650.17660.00790.00880.16330.00880.13169.8575.39711.849
51.11520.574-0.03012.56710.37030.90430.01080.1-0.02670.18920.0512-0.21710.04690.052-0.04920.08580.0173-0.01310.11910.00340.093317.7379.4587.778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2917:2944 )A2917 - 2944
2X-RAY DIFFRACTION2( CHAIN A AND RESID 2945:2973 )A2945 - 2973
3X-RAY DIFFRACTION3( CHAIN A AND RESID 2974:2988 )A2974 - 2988
4X-RAY DIFFRACTION4( CHAIN A AND RESID 2989:3011 )A2989 - 3011
5X-RAY DIFFRACTION5( CHAIN A AND RESID 3012:3036 )A3012 - 3036

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