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- PDB-2kwk: Solution structures of the double PHD fingers of human transcript... -

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Basic information

Entry
Database: PDB / ID: 2kwk
TitleSolution structures of the double PHD fingers of human transcriptional protein DPF3b bound to a H3 peptide wild type
Components
  • Histone peptide
  • Zinc finger protein DPF3
KeywordsMETAL BINDING PROTEIN / acetyl-lysine / Transcription regulation / Nucleus
Function / homology
Function and homology information


brahma complex / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / muscle organ development / positive regulation of double-strand break repair / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation ...brahma complex / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / muscle organ development / positive regulation of double-strand break repair / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / 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 / HDACs deacetylate histones / positive regulation of cell differentiation / 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 / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / PHD-finger / 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 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Zinc finger protein DPF3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
Model detailslowest energy, model 20
AuthorsZeng, L. / Zhang, Q. / Li, S. / Plotnikov, A.N. / Walsh, M.J. / Zhou, M.
CitationJournal: Nature / Year: 2010
Title: Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.
Authors: Zeng, L. / Zhang, Q. / Li, S. / Plotnikov, A.N. / Walsh, M.J. / Zhou, M.M.
History
DepositionApr 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Histone peptide
A: Zinc finger protein DPF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1996
Polymers14,9372
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Histone peptide


Mass: 2190.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: P68431*PLUS
#2: Protein Zinc finger protein DPF3 / / Zinc finger protein cer-d4 / BRG1-associated factor 45C / BAF45C


Mass: 12746.472 Da / Num. of mol.: 1 / Fragment: PHD-types 1 and 2 residues 261-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF3, BAF45C, CERD4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92784
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D 13C-Edited 13C/15N-filtered NOEST
1413D HN(CA)CB
1513D HN(COCA)CB
NMR detailsText: The structures were determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 100 mM potassium phosphate, 2 mM DTT, 100% D2O / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMpotassium phosphate-11
2 mMDTT-21
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Bruker AvanceBrukerAvance8002
Bruker AvanceBrukerAvance6003
Bruker DRXBrukerDRX5004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.04Johnson, One Moon Scientificdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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