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- PDB-7kdw: Crystal structure of the bromodomain (BD) of human Bromodomain an... -

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Basic information

Entry
Database: PDB / ID: 7kdw
TitleCrystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to Compound 6 (HZ01052)
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION / BRD / PHD / FAC1 / FALZ / nucleosome-remodeling factor subunit
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 / 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
Similarity search - Domain/homology
Chem-WCV / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsChan, A. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM121414-01 United States
CitationJournal: Organic and Biomolecular Chemistry / Year: 2020
Title: New inhibitors for the BPTF bromodomain enabled by structural biology and biophysical assay development
Authors: Ycas, P.D. / Zahid, H. / Chan, A. / Olson, N.M. / Johnson, J.A. / Talluri, S.K. / Schonbrunn, E. / Pomerantz, W.C.K.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)29,6685
Polymers28,9112
Non-polymers7573
Water2,792155
1
A: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8653
Polymers14,4551
Non-polymers4092
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)14,8032
Polymers14,4551
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.220, 37.960, 57.070
Angle α, β, γ (deg.)96.630, 103.820, 90.880
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
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) / Strain (production host): BL21(DE3) / References: UniProt: Q12830
#2: Chemical ChemComp-WCV / cyclopropyl[7-({2-[(prop-2-yn-1-yl)amino]pyrimidin-4-yl}amino)-3,4-dihydroquinolin-1(2H)-yl]methanone


Mass: 347.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.97 Å3/Da / Density % sol: 37.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH6.5, 25 percent polyethylene glycol 3,350

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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: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→33.02 Å / Num. obs: 23629 / % possible obs: 99.3 % / Redundancy: 12.745 % / Biso Wilson estimate: 24.629 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.214 / Rrim(I) all: 0.222 / Χ2: 0.777 / Net I/σ(I): 11.82 / Num. measured all: 301156 / Scaling rejects: 638
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.71-1.755.1130.4113.028804173117220.9070.4699.5
1.75-1.85.4510.4153.449425174617290.8960.45999
1.8-1.859.0990.4054.7814931165716410.960.4399
1.85-1.9112.30.3896.2319913162616190.9770.40699.6
1.91-1.9712.7280.3476.9519703157115480.9830.36298.5
1.97-2.0414.3510.3169.0121397149914910.9850.32799.5
2.04-2.1214.9190.31510.2222006149514750.9840.32798.7
2.12-2.2114.920.27811.8120903140614010.9860.28999.6
2.21-2.3114.9730.26913.2720124135913440.9810.27998.9
2.31-2.4214.9610.25614.0918806126012570.9840.26699.8
2.42-2.5515.060.25915.4918735125112440.990.26899.4
2.55-2.714.9960.23616.217605118711740.9920.24598.9
2.7-2.8915.0180.2317.4316249108510820.9940.23899.7
2.89-3.1214.8470.2318.514981101810090.9810.23999.1
3.12-3.4214.6320.22620.1137399399390.9950.234100
3.42-3.8214.2340.18820.95120288498450.9970.19599.5
3.82-4.4215.4020.18822.05112907337330.9980.195100
4.42-5.4115.3920.16622.1597746386350.9980.17299.5
5.41-7.6515.1290.13321.9372624824800.9980.13899.6
7.65-33.0213.3370.11421.5634812662610.9980.1298.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV2

3uv2


Resolution: 1.71→33.02 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 31.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1182 5 %
Rwork0.2015 22443 -
obs0.2038 23625 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.19 Å2 / Biso mean: 25.3435 Å2 / Biso min: 8.77 Å2
Refinement stepCycle: final / Resolution: 1.71→33.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 56 155 2099
Biso mean--26.7 30.94 -
Num. residues----227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.790.37361470.30232788293599
1.79-1.880.30461460.25872777292399
1.88-20.31691480.24272811295999
2-2.150.28231480.21182813296199
2.15-2.370.25821480.21442818296699
2.37-2.710.24591490.20462826297599
2.71-3.420.26551480.198628022950100
3.42-33.020.17751480.159428082956100
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)
12.9969-1.4931-0.67794.32841.28923.2323-0.08770.05760.3864-0.27640.1972-0.2006-0.58870.2765-0.12660.35620.01880.00140.2617-0.02750.105113.651821.1708-8.6909
26.66790.1629-2.36081.5235-0.66345.2915-0.13830.0204-0.5936-0.030.00980.20370.2109-0.18790.11450.20790.0387-0.0040.1466-0.00010.10374.09134.27062.4417
35.14351.93470.66686.47110.7197.57990.00230.25590.2395-0.0569-0.05440.2271-0.0713-0.14490.05910.14370.06070.00540.14910.00120.07264.284519.1569-6.8773
41.86381.02-0.59461.9771-0.8992.6399-0.0181-0.1414-0.09440.0689-0.0201-0.105-0.00890.11290.03050.1280.0617-0.00130.2132-0.01180.08814.110312.43063.809
51.74821.45931.53114.26491.27992.4197-0.01260.034-0.28230.2820.2075-0.26940.53860.2601-0.17030.32820.04090.04610.2536-0.0390.1460.36695.5058-18.8846
66.41830.19153.36341.2891-0.18556.1175-0.3030.10620.563-0.01040.08290.1651-0.1814-0.22730.14290.18430.01390.02690.14410.00980.1045-9.578422.9772-29.4015
73.37440.22240.0744.281-1.59526.32210.0645-0.2076-0.1010.1013-0.01270.19530.0813-0.1614-0.05950.12670.00760.03250.14730.01350.0661-9.21818.179-20.0327
81.4616-0.21690.47761.2351-0.21031.52580.02010.090.0316-0.1023-0.0019-0.0656-0.05330.105-0.01650.17090.00760.03670.1962-0.01380.08740.768514.9728-30.7151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2923 through 2945 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2946 through 2973 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2974 through 2988 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2989 through 3035 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2922 through 2945 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 2946 through 2973 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 2974 through 2988 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 2989 through 3035 )B0

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