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- PDB-7lro: Crystal structure of BPTF bromodomain in complex with inhibitor H... -

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Basic information

Entry
Database: PDB / ID: 7lro
TitleCrystal structure of BPTF bromodomain in complex with inhibitor HZ-01-105
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION/INHIBITOR / BPTF / bromodomain / inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex
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-YBV / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
Model detailsCocrystal structure of BPTF bromodomain
AuthorsChan, A. / Schonbrunn, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121414-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30-CA076292 United States
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
DepositionFeb 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 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
Revision 1.2Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)30,16317
Polymers28,9112
Non-polymers1,25215
Water6,593366
1
A: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0598
Polymers14,4551
Non-polymers6037
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)15,1059
Polymers14,4551
Non-polymers6498
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.410, 27.070, 76.920
Angle α, β, γ (deg.)90.000, 93.870, 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.: 2 / 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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12830
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-YBV / 5-(azetidin-3-ylamino)-4-chloranyl-2-methyl-pyridazin-3-one


Mass: 214.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11ClN4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→33.1 Å / Num. obs: 43259 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.082 / Net I/σ(I): 14
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3165 / CC1/2: 0.782 / Rrim(I) all: 0.586 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K6R

7k6r


Resolution: 1.45→33.09 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 1200 2.77 %
Rwork0.1592 42056 -
obs0.16 43256 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.81 Å2 / Biso mean: 13.647 Å2 / Biso min: 4.03 Å2
Refinement stepCycle: final / Resolution: 1.45→33.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 80 366 2426
Biso mean--17.66 24.07 -
Num. residues----241
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 (%)
1.45-1.510.25311320.215346414773100
1.51-1.580.21551310.187245994730100
1.58-1.660.21861320.178346344766100
1.66-1.760.20131320.174646204752100
1.76-1.90.2321330.160246624795100
1.9-2.090.18911340.15846804814100
2.09-2.390.19081330.141146564789100
2.39-3.020.17821340.152147254859100
3.02-33.090.16061390.14894839497899
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)
18.0597-0.95033.16123.5331-1.02865.73440.15120.32440.362-0.1137-0.18070.0315-0.60410.01120.02720.18120.00040.02870.10820.01180.0617-9.84072.8641-19.1115
20.95551.41680.07372.23650.75244.633-0.03750.0470.0383-0.12840.1374-0.06470.06460.2615-0.05550.04230.0161-0.00680.06950.00570.0906-2.34270.6666-4.0816
33.8674.9862-0.75987.0301-1.67851.00590.309-0.29620.08660.5288-0.26190.1587-0.00770.0333-0.02320.0987-0.00140.00890.0832-0.00510.0676-16.2482-6.67589.7262
46.53931.9262-2.40731.1548-0.61211.34060.00130.1143-0.13290.0609-0.0131-0.06050.03280.00640.02460.0530.0028-0.00660.0315-0.0040.0591-13.8065-11.0856-0.5633
55.2381-4.24182.82015.9595-3.35153.43610.10560.2769-0.0631-0.2369-0.2177-0.1110.16490.25280.0760.06680.00030.02160.065-0.00580.0801-4.4399-9.0959-11.1762
62.15860.653-1.08291.7132-0.12841.16510.00210.00390.0296-0.06150.0074-0.0185-0.04390.0084-0.00870.04030.0092-0.02220.04060.00510.0348-17.04680.9897-1.835
70.89030.55940.07450.5367-0.26226.1962-0.07680.0814-0.0464-0.14360.01750.06940.1812-0.22990.0730.0921-0.006-0.01680.06340.0020.088-21.62742.1528-48.6287
83.48922.855-0.69073.0121-0.47421.45130.1384-0.18780.08930.2583-0.1380.0189-0.10950.02390.00150.06390.013-0.00570.0645-0.00690.0674-8.779212.9806-32.1214
93.3956-0.65461.78951.0695-0.31511.583-0.02290.01110.0383-0.04880.01720.047-0.0366-0.00520.01050.0534-0.0110.0110.02770.00480.0491-14.223910.3556-43.1768
103.10880.86591.74541.91620.26672.2660.08060.0144-0.1525-0.0650.0159-0.02820.17090.0009-0.11170.05850.00560.02090.03390.00720.0496-10.8932-0.9027-39.5057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2917 through 2929 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2930 through 2945 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2946 through 2963 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2964 through 2982 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 2983 through 2988 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 2989 through 3036 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 2917 through 2945 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 2946 through 2973 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 2974 through 3006 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 3007 through 3037 )B0

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