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- PDB-8ou2: Crystal structure of the bromodomain of human Bromodomain and PHD... -

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Basic information

Entry
Database: PDB / ID: 8ou2
TitleCrystal structure of the bromodomain of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to a potent inhibitor
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsTRANSCRIPTION / Nucleosome-remodeling factor subunit BPTF / inhibitor
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
: / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBalikci, E. / Ni, X. / Bountra, C. / von Delft, F. / Huber, K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the bromodomain of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to a potent inhibitor
Authors: Balikci, E. / Ni, X. / Bountra, C. / von Delft, F. / Huber, K.
History
DepositionApr 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)30,55912
Polymers28,9112
Non-polymers1,64810
Water6,377354
1
A: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2395
Polymers14,4551
Non-polymers7844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3197
Polymers14,4551
Non-polymers8646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.277, 27.043, 77.637
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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 (E. coli) / References: UniProt: Q12830

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Non-polymers , 5 types, 364 molecules

#2: Chemical ChemComp-W2W / 7-(1-cyclopropylpyrazol-4-yl)-2-[[2-fluoranyl-4-(4-methylpiperazin-1-yl)sulfonyl-phenyl]amino]-3-methyl-pyrido[1,2-a]pyrimidin-4-one


Mass: 537.609 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28FN7O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.20M KSCN; 0.1M BTProp pH 6.5; 20.0% PEG 3350; 10.0% EtGly

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→77.494 Å / Num. obs: 200470 / % possible obs: 95.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 10.8
Reflection shellResolution: 1.601→1.648 Å / Num. unique obs: 8233 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→77.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.169 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22243 1540 5.2 %RANDOM
Rwork0.18052 ---
obs0.18268 27919 90.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.02 Å2
2--0.02 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.6→77.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 112 354 2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152005
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.6742969
X-RAY DIFFRACTIONr_angle_other_deg1.4291.5824635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48921.885122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77115363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1181516
X-RAY DIFFRACTIONr_chiral_restr0.080.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02508
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.057983
X-RAY DIFFRACTIONr_mcbond_other0.9071.055982
X-RAY DIFFRACTIONr_mcangle_it1.3511.5751230
X-RAY DIFFRACTIONr_mcangle_other1.3521.5771231
X-RAY DIFFRACTIONr_scbond_it1.7021.3171209
X-RAY DIFFRACTIONr_scbond_other1.7021.3181210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5271.891733
X-RAY DIFFRACTIONr_long_range_B_refined4.42414.3652815
X-RAY DIFFRACTIONr_long_range_B_other4.42414.3652815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3959 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 67 -
Rwork0.253 1228 -
obs--54.73 %

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