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- PDB-7k6s: Crystal structure of the bromodomain (BD) of human Bromodomain an... -

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Basic information

Entry
Database: PDB / ID: 7k6s
TitleCrystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to Compound 4 (SKT1174)
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 / 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-VYM / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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)14,8615
Polymers14,4551
Non-polymers4064
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.210, 27.210, 37.920
Angle α, β, γ (deg.)90.000, 96.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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 / Plasmid: pNIC28-Bsa1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12830

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Non-polymers , 5 types, 131 molecules

#2: Chemical ChemComp-VYM / (7-amino-3,4-dihydroquinolin-1(2H)-yl)(cyclopropyl)methanone


Mass: 216.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 37.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M 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: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.23→32.99 Å / Num. obs: 32926 / % possible obs: 99.3 % / Redundancy: 3.563 % / Biso Wilson estimate: 16.562 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.041 / Χ2: 0.999 / Net I/σ(I): 22.91 / Num. measured all: 117307 / Scaling rejects: 37
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
1.23-1.263.0230.1586.487216241923870.9730.19298.7
1.26-1.33.5630.138.568455240123730.9850.15398.8
1.3-1.333.5940.11410.058140227722650.9870.13499.5
1.33-1.383.5720.09511.777922223122180.990.11299.4
1.38-1.423.5910.0813.497746216421570.9920.09599.7
1.42-1.473.590.06516.197590212121140.9950.07799.7
1.47-1.533.6040.05519.117233201720070.9960.06599.5
1.53-1.593.6220.04622.27103196719610.9970.05599.7
1.59-1.663.640.04224.656800187318680.9970.04999.7
1.66-1.743.6320.03826.756502179317900.9980.04499.8
1.74-1.833.6430.03529.626223171217080.9980.04199.8
1.83-1.943.6410.03232.765920164016260.9980.03899.1
1.94-2.083.6360.03135.145454151315000.9980.03799.1
2.08-2.253.5960.0337.15099142714180.9980.03599.4
2.25-2.463.6570.0338.944835132413220.9980.03599.8
2.46-2.753.6120.0339.224244119011750.9980.03698.7
2.75-3.183.6240.0340.343780105610430.9970.03598.8
3.18-3.893.6240.0341.4732809139050.9980.03699.1
3.89-5.53.5220.03341.224627076990.9970.03998.9
5.5-32.993.3410.03439.3113034083900.9970.04195.6

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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: 1.23→32.99 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 1199 3.64 %
Rwork0.1646 31727 -
obs0.166 32926 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.41 Å2 / Biso mean: 19.4006 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: final / Resolution: 1.23→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 27 127 1120
Biso mean--28.57 30.34 -
Num. residues----117
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 (%)
1.23-1.280.20381310.20163467359899
1.28-1.340.21181310.18433473360499
1.34-1.410.18831330.17135223655100
1.41-1.50.19321320.162434983630100
1.5-1.610.19061340.156935303664100
1.61-1.770.21521320.158935093641100
1.77-2.030.17541340.16213551368599
2.03-2.560.18561350.16063552368799
2.56-32.990.22361370.16443625376299
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)
11.4260.20560.37531.4994-0.06942.771-0.0032-0.29410.10330.2474-0.05170.0351-0.0977-0.0665-0.01970.0783-0.0023-0.00240.2008-0.0130.1621-22.99670.82729.2128
23.2123-1.10560.57733.408-0.65761.3510.23630.57580.0094-0.4717-0.3006-0.18710.15320.13730.06490.09860.03870.02030.22950.02140.1326-12.9545-5.9627-10.5696
31.92810.8828-1.10070.6034-0.07671.5559-0.0635-0.0912-0.2515-0.00510.0137-0.06440.11230.05350.00340.0029-0.0095-0.01130.13950.02730.1866-14.2272-11.1254-0.1833
46.46764.14381.51034.26041.6742.72040.1758-0.4185-0.09810.2103-0.18650.04880.081-0.1508-0.07780.06-0.0111-0.00030.14470.0170.1185-22.6032-9.632311.0878
54.3414-1.047-2.83110.71210.61922.3280.0466-0.12330.0597-0.0037-0.0079-0.1152-0.0460.1448-0.08820.0302-0.0109-0.00880.13260.0120.1433-9.4286-4.17033.1238
62.2465-1.0509-1.29351.45870.52891.94080.0140.00350.1030.0084-0.0127-0.1209-0.09530.0783-0.04950.044-0.0132-0.01180.12720.02020.1636-10.91644.6932-0.8409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2919 through 2945 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2946 through 2963 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2964 through 2982 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2983 through 2988 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 2989 through 3006 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 3007 through 3035 )A0

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