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

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Basic information

Entry
Database: PDB / ID: 7kdz
TitleCrystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to TP-238
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION / BRD / PHD / FAC1 / FALZ
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-WCS / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 & 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9763
Polymers14,4551
Non-polymers5212
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.670, 42.670, 126.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-WCS / 6-{4-[3-(dimethylamino)propoxy]phenyl}-2-(methylsulfonyl)-N-[3-(1H-pyrazol-1-yl)propyl]pyrimidin-4-amine


Mass: 458.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N6O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 290 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: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→31.71 Å / Num. obs: 18158 / % possible obs: 99.8 % / Redundancy: 14.068 % / Biso Wilson estimate: 28.963 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Χ2: 1.039 / Net I/σ(I): 18.45 / Num. measured all: 255441
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
1.54-1.5813.8460.9253.1318194131513140.8830.96199.9
1.58-1.6212.8770.7863.6616238126912610.9080.81999.4
1.62-1.6714.350.6564.617938125312500.9480.6899.8
1.67-1.7214.9380.5066.0617926120212000.9680.52499.8
1.72-1.7814.8270.3977.417689119311930.9850.412100
1.78-1.8414.8540.3179.2816711112511250.9870.329100
1.84-1.9114.6760.25811.216173110511020.9890.26799.7
1.91-1.9914.4390.19313.9815248105810560.9930.299.8
1.99-2.0814.1380.15117.3314463102410230.9950.15799.9
2.08-2.1813.6370.11621.34133789829810.9970.1299.9
2.18-2.312.470.10321.95115859379290.9970.10799.1
2.3-2.4314.9350.08928.26133528958940.9980.09299.9
2.43-2.614.8540.08230.22125078428420.9980.085100
2.6-2.8114.6190.0733.41115057887870.9980.07399.9
2.81-3.0814.2630.06436.71105267387380.9990.066100
3.08-3.4413.8560.05839.7692566686680.9980.06100
3.44-3.9812.8120.0542.477136026020.9990.052100
3.98-4.8712.3550.04742.7163635205150.9990.04999
4.87-6.8913.6350.04645.0656864184170.9990.04799.8
6.89-31.7111.4560.04141.8829902622610.9990.04399.6

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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: 1.54→31.71 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1100 6.06 %
Rwork0.1853 17055 -
obs0.1865 18155 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.69 Å2 / Biso mean: 29.1743 Å2 / Biso min: 15.2 Å2
Refinement stepCycle: final / Resolution: 1.54→31.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 36 80 996
Biso mean--25.13 40.03 -
Num. residues----105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.54-1.610.26021330.236920582191
1.61-1.690.27241350.207620872222
1.7-1.80.23081340.190420862220
1.8-1.940.18311360.171521132249
1.94-2.140.18981360.170321002236
2.14-2.440.18261370.172821252262
2.44-3.080.19981400.196521732313
3.08-31.710.20911490.183523132462
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)
13.3335-0.1146-1.1653.5346-1.3893.643-0.11510.0239-0.2517-0.12360.0953-0.09940.1723-0.11660.02930.1256-0.0346-0.01110.1379-0.03350.171712.60160.3882137.914
22.01330.8538-1.23965.7195-2.5673.6509-0.11590.1572-0.5179-0.384-0.1304-0.25810.2846-0.06590.16760.20270.0050.04130.1675-0.04020.253420.3757-2.3275133.6385
31.9461.6698-0.58396.1628-2.84712.5956-0.0221-0.0161-0.27650.0396-0.0726-0.25490.02070.10860.16980.15580.0119-0.00360.17840.00860.246221.55131.5043140.2795
44.60170.2615-1.41914.0894-1.55756.6793-0.1727-0.2972-0.27060.3756-0.1-0.2727-0.07710.14420.25510.13170.0146-0.03430.12620.00770.138415.07519.0839144.8724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2927 through 2963 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2964 through 2982 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2983 through 3011 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 3012 through 3031 )A0

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