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- PDB-7k6r: Crystal structure of the bromodomain (BD) of human Bromodomain an... -

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Basic information

Entry
Database: PDB / ID: 7k6r
TitleCrystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to GSK4027
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-9ST / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Org.Biomol.Chem. / 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
DepositionSep 21, 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)14,9574
Polymers14,4551
Non-polymers5013
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.060, 35.520, 41.150
Angle α, β, γ (deg.)114.120, 95.930, 91.060
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.: 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-9ST / 4-bromo-2-methyl-5-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]pyridazin-3-one


Mass: 377.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21BrN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1M BIS-TRIS, 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: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→37.28 Å / Num. obs: 17236 / % possible obs: 93.8 % / Redundancy: 1.83 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.05 / Χ2: 0.991 / Net I/σ(I): 12.84 / Num. measured all: 31539 / Scaling rejects: 2
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
1.6-1.641.8980.2183.372395135012620.8660.30893.5
1.64-1.691.8590.1793.742318134412470.9160.25392.8
1.69-1.741.8390.1524.282144126811660.9390.21492
1.74-1.791.8140.1295.132182127312030.9580.18394.5
1.79-1.851.710.1085.961914119211190.9670.15393.9
1.85-1.911.7420.0957.131908116310950.9740.13494.2
1.91-1.981.8670.0749.031975114210580.9860.10492.6
1.98-2.071.9060.05911.311980110010390.990.08394.5
2.07-2.161.8740.0513.65183110329770.9920.0794.7
2.16-2.261.8580.04315.217459989390.9940.0694.1
2.26-2.391.8150.0416.4616399529030.9940.05694.9
2.39-2.531.760.03717.2914708918350.9950.05293.7
2.53-2.71.7230.03318.9113638497910.9960.04693.2
2.7-2.921.8580.0322.2113867897460.9950.04294.6
2.92-3.21.9280.02824.5313177236830.9960.0494.5
3.2-3.581.8830.02526.811796536260.9960.03695.9
3.58-4.131.8460.02428.359935695380.9970.03394.6
4.13-5.061.6970.02227.047944984680.9980.03194
5.06-7.161.8390.02127.636513773540.9980.0393.9
7.16-37.281.8980.02130.973552031870.9980.0392.1

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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: 1.6→37.28 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 1104 6.41 %
Rwork0.1613 16131 -
obs0.1636 17235 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.36 Å2 / Biso mean: 22.4985 Å2 / Biso min: 11.23 Å2
Refinement stepCycle: final / Resolution: 1.6→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 31 167 1205
Biso mean--22.49 31.68 -
Num. residues----122
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 (%)
1.6-1.670.21291370.18982003214093
1.67-1.760.23581350.18731975211093
1.76-1.870.23971390.18772029216894
1.87-2.020.24221380.18172017215594
2.02-2.220.20861390.16392036217595
2.22-2.540.20961380.16522012215094
2.54-3.20.19061380.15792027216594
3.2-37.280.16231400.14252032217295
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)
17.0925-0.86881.28985.33921.83845.1714-0.03910.39980.1936-0.43740.0502-0.3977-0.20560.6963-0.0340.1693-0.01490.00470.2227-0.01770.124717.3909-14.6386-27.4187
21.4072-0.506-0.12993.43682.17713.33520.0512-0.1119-0.05940.2045-0.08040.03630.1522-0.10640.01080.129-0.03040.01320.13890.04890.130811.0707-9.7737-6.0053
31.0332-0.3570.22553.76271.37412.2299-0.04960.00440.051-0.02390.02040.1354-0.1298-0.01290.04050.10230.0007-0.01110.14130.01940.15796.6037-4.7739-12.3256
42.3085-0.7437-0.39033.56462.41333.51120.01740.02190.0485-0.01640.0582-0.1882-0.08180.1058-0.14110.1101-0.0195-0.01350.14170.03250.126119.8142-6.6355-12.2749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2916 through 2929 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2930 through 2963 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2964 through 3011 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 3012 through 3037 )A0

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