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- PDB-5c7n: Crystal structure of the human BRPF1 bromodomain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5c7n
TitleCrystal structure of the human BRPF1 bromodomain in complex with Bromosporine
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1 / histone acetyltransferase(HAT) / transferase
Function / homology
Function and homology information


acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / 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 / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / 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 / metal ion binding / nucleus / 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. / domain with conserved PWWP motif ...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 / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZhu, J. / Caflisch, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions.
Authors: Zhu, J. / Caflisch, A.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1703
Polymers13,7041
Non-polymers4662
Water1,838102
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint2 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.502, 60.502, 63.111
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-958-

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 / Fragment: residues 626-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N6O4S
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


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


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3350, 0.1 M sodium acetate, 0.15 M sodium nitrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: PSI PILATUS 2M / Detector: PIXEL / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.75→40.31 Å / Num. all: 134208 / Num. obs: 13890 / % possible obs: 100 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.75→40.31 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 710 5.12 %
Rwork0.1809 --
obs0.183 13867 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 32 102 1064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011023
X-RAY DIFFRACTIONf_angle_d0.9871387
X-RAY DIFFRACTIONf_dihedral_angle_d13.934408
X-RAY DIFFRACTIONf_chiral_restr0.039144
X-RAY DIFFRACTIONf_plane_restr0.004183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.88520.28911220.22922602X-RAY DIFFRACTION100
1.8852-2.07490.231390.2082581X-RAY DIFFRACTION100
2.0749-2.37510.24871600.19162592X-RAY DIFFRACTION100
2.3751-2.99220.20411340.20732649X-RAY DIFFRACTION100
2.9922-40.32420.21421550.16042733X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.3988 Å / Origin y: 1.6383 Å / Origin z: -10.0069 Å
111213212223313233
T0.4068 Å20.0719 Å2-0.0435 Å2-0.1738 Å2-0.0198 Å2--0.2381 Å2
L4.458 °2-0.3039 °21.3464 °2-3.3744 °20.8826 °2--2.4862 °2
S-0.2266 Å °-0.4161 Å °0.0017 Å °0.6192 Å °0.1072 Å °-0.1232 Å °0.0998 Å °-0.0592 Å °0.1032 Å °
Refinement TLS groupSelection details: all

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