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- PDB-2m0o: The solution structure of human PHF1 in complex with H3K36me3 -

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Basic information

Entry
Database: PDB / ID: 2m0o
TitleThe solution structure of human PHF1 in complex with H3K36me3
Components
  • H3K36me3 peptide
  • PHD finger protein 1
KeywordsPEPTIDE BINDING PROTEIN / Tudor Domain / H3K36me3 binding
Function / homology
Function and homology information


histone methyltransferase binding / DNA repair-dependent chromatin remodeling / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation ...histone methyltransferase binding / DNA repair-dependent chromatin remodeling / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / 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 / transcription corepressor binding / 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 / 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 / site of double-strand break / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 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 / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / centrosome / chromatin binding / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
: / : / PHD finger protein 1 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 ...: / : / PHD finger protein 1 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / 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 / SH3 type barrels. / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
PHD finger protein 1 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsSong, J. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2013
Title: An H3K36 Methylation-Engaging Tudor Motif of Polycomb-like Proteins Mediates PRC2 Complex Targeting.
Authors: Cai, L. / Rothbart, S.B. / Lu, R. / Xu, B. / Chen, W.Y. / Tripathy, A. / Rockowitz, S. / Zheng, D. / Patel, D.J. / Allis, C.D. / Strahl, B.D. / Song, J. / Wang, G.G.
History
DepositionOct 30, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 1
B: H3K36me3 peptide


Theoretical massNumber of molelcules
Total (without water)9,9972
Polymers9,9972
Non-polymers00
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PHD finger protein 1 / / Protein PHF1 / Polycomb-like protein 1 / hPCl1


Mass: 8737.847 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF1, PCL1 / Plasmid: PRSF-Duet / Production host: Escherichia coli (E. coli) / References: UniProt: O43189
#2: Protein/peptide H3K36me3 peptide


Mass: 1259.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P68431*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aliphatic
1213D 1H-13C NOESY aromatic
1312D 1H-15N HSQC
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1812D 1H-1H NOESY
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.3-0.5 mM [U-100% 13C; U-100% 15N] PHF1 tudor, 0.6-1.0 mM H3K36me3 peptide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMPHF1 tudor-1[U-100% 13C; U-100% 15N]0.3-0.51
mMH3K36me3 peptide-20.6-1.01
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX9001
Bruker DMXBrukerDMX7002
Bruker DMXBrukerDMX6003

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Processing

NMR softwareName: X-PLOR_NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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