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- PDB-6u04: Crystal structure of human BRPF1 PZP bound to histone H3 tail -

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Basic information

Entry
Database: PDB / ID: 6u04
TitleCrystal structure of human BRPF1 PZP bound to histone H3 tail
ComponentsHistone H3.3,BRPF1, Peregrin
KeywordsTRANSCRIPTION / epigenetics / nucleosome / DNA binding
Function / homology
Function and homology information


acetyltransferase activator activity / nucleosomal DNA binding / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Regulation of TP53 Activity through Acetylation / Inhibition of DNA recombination at telomere ...acetyltransferase activator activity / nucleosomal DNA binding / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Regulation of TP53 Activity through Acetylation / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / 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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PRASEODYMIUM ION / Peregrin / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKlein, B.J. / Kutateladze, T.G.
CitationJournal: Structure / Year: 2020
Title: Molecular Basis for the PZP Domain of BRPF1 Association with Chromatin.
Authors: Klein, B.J. / Cox, K.L. / Jang, S.M. / Cote, J. / Poirier, M.G. / Kutateladze, T.G.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Histone H3.3,BRPF1, Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5347
Polymers22,0661
Non-polymers4686
Water1,946108
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: assay for oligomerization, HSQC NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.461, 72.461, 155.297
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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Components

#1: Protein Histone H3.3,BRPF1, Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 22066.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P84243, UniProt: P55201
#2: Chemical ChemComp-PR / PRASEODYMIUM ION / Praseodymium


Mass: 140.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pr
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.5, 40% (v/v) PEG400, and 0.01M Praseodymium(III) acetate hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.196→50 Å / Num. obs: 12975 / % possible obs: 99.5 % / Redundancy: 20.8 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.032 / Rrim(I) all: 0.148 / Χ2: 1.115 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2820.70.79412490.9160.1770.8140.956100
2.28-2.3722.30.62112630.9340.1330.6360.92100
2.37-2.4822.90.512660.9690.1050.5110.944100
2.48-2.6123.60.43812690.9770.0910.4470.969100
2.61-2.7724.50.31712800.9880.0650.3241.04100
2.77-2.9924.50.22812850.9920.0460.2331.138100
2.99-3.2915.70.16212940.9920.0410.1681.15499.8
3.29-3.769.40.09312780.9940.0280.0971.27397.8
3.76-4.7422.80.08313450.9990.0170.0851.736100
4.74-5021.40.06614460.9990.0140.0671.08298.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ERC

5erc


Resolution: 2.2→22.684 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.56
RfactorNum. reflection% reflection
Rfree0.2085 1274 9.97 %
Rwork0.1718 --
obs0.1756 12773 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.27 Å2 / Biso mean: 37.8683 Å2 / Biso min: 17.38 Å2
Refinement stepCycle: final / Resolution: 2.2→22.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 6 108 1412
Biso mean--35.27 41.45 -
Num. residues----168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.28410.27561340.2053122197
2.2841-2.3880.2381370.1925122599
2.388-2.51370.24311360.1854124297
2.5137-2.6710.2191370.1758123798
2.671-2.87680.23581400.1778125999
2.8768-3.16560.21111440.16941289100
3.1656-3.62210.19681410.1583127498
3.6221-4.55740.17141470.14491325100
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)
12.3052-0.0841-1.180.80050.03652.144-0.18630.2581-0.240.04810.02980.01650.2282-0.11650.1130.3019-0.04670.0610.204-0.00270.2071.341522.2796-10.21
27.6177-1.444-4.28410.6780.08753.708-0.5008-0.9315-0.25232.8105-0.13171.50470.948-0.38040.62361.2113-0.13940.27530.5823-0.31440.874310.94483.358-13.5619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 274 through 451)A274 - 451
2X-RAY DIFFRACTION2(chain 'A' and resid 1 through 3)A1 - 3

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