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- PDB-8qaz: Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyr... -

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Basic information

Entry
Database: PDB / ID: 8qaz
TitleCrystal Structure of BRPF1 bromodomain in complex with acetyl-pyrrole derivative compound 3
ComponentsPeregrin
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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
NITRATE ION / : / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: To be published
Title: Dual BET/BRPF1 inhibitors induce morphological alteration and cellular death in various human cancer cell lines
Authors: Cazzanelli, G. / Dalle Vedove, A. / Caflisch, A. / Lolli, G.
History
DepositionAug 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0993
Polymers13,7041
Non-polymers3952
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint1 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.552, 60.552, 62.507
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-962-

HOH

21A-973-

HOH

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 1 / Mutation: bromodomain (residues 626-740)
Source method: isolated from a genetically manipulated source
Details: First residue S derives from the expression tag / Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P55201
#2: Chemical ChemComp-QA5 / 2-[4-[4-ethanoyl-5-methyl-3-(3-methylbutyl)-1~{H}-pyrrol-2-yl]-1,3-thiazol-2-yl]guanidine


Mass: 333.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.18 M sodium nitrate, 30% PEG 3350, 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→62.51 Å / Num. obs: 26585 / % possible obs: 100 % / Redundancy: 18.2 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.01 / Rrim(I) all: 0.04 / Χ2: 1.01 / Net I/σ(I): 33.8 / Num. measured all: 484174
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 17.6 % / Rmerge(I) obs: 1.567 / Num. measured all: 22510 / Num. unique obs: 1282 / CC1/2: 0.768 / Rpim(I) all: 0.383 / Rrim(I) all: 1.614 / Χ2: 1.01 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→52.44 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 1327 5 %
Rwork0.1629 --
obs0.1645 26550 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→52.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 27 105 1075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081031
X-RAY DIFFRACTIONf_angle_d0.9151396
X-RAY DIFFRACTIONf_dihedral_angle_d27.836410
X-RAY DIFFRACTIONf_chiral_restr0.061145
X-RAY DIFFRACTIONf_plane_restr0.005186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.45620.26091530.21712764X-RAY DIFFRACTION100
1.4562-1.52250.22331400.16692760X-RAY DIFFRACTION100
1.5225-1.60270.20391570.15442756X-RAY DIFFRACTION100
1.6027-1.70310.16741530.14972773X-RAY DIFFRACTION100
1.7031-1.83470.1961410.14842786X-RAY DIFFRACTION100
1.8347-2.01930.20191200.16252808X-RAY DIFFRACTION100
2.0193-2.31150.19091490.15822796X-RAY DIFFRACTION100
2.3115-2.91220.20521670.17222834X-RAY DIFFRACTION100
2.9122-52.440.18891470.16112946X-RAY DIFFRACTION100

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