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- PDB-4bd3: Phf19 links methylated lysine 36 of histone H3 to regulation of P... -

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Basic information

Entry
Database: PDB / ID: 4bd3
TitlePhf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity
Components
  • HISTONE H3
  • PHD FINGER PROTEIN 19
KeywordsTRANSCRIPTION / PHF-19 / HISTONE RECOGNITION / H3K36ME3
Function / homology
Function and homology information


ESC/E(Z) complex / negative regulation of gene expression, epigenetic / stem cell population maintenance / 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 ...ESC/E(Z) complex / negative regulation of gene expression, epigenetic / stem cell population maintenance / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / stem 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding
Similarity search - Function
PHF19, PHD domain 2 / : / 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 ...PHF19, PHD domain 2 / : / 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-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
Histone H3.1 / PHD finger protein 19
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA
AuthorsLapinaite, A. / Simon, B. / Carlomagno, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Phf19 Links Methylated Lys36 of Histone H3 to Regulation of Polycomb Activity
Authors: Ballare, C. / Lange, M. / Lapinaite, A. / Mas Martin, G. / Morey, L. / Pascu, G. / Liefke, R. / Simon, B. / Shi, Y. / Gozani, O. / Carlomagno, T. / Benitah, S.A. / Di Croce, L.
History
DepositionOct 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Atomic model / Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD FINGER PROTEIN 19
B: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)7,9812
Polymers7,9812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #6

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Components

#1: Protein PHD FINGER PROTEIN 19 / POLYCOMB-LIKE PROTEIN 3 / HPCL3


Mass: 6721.652 Da / Num. of mol.: 1 / Fragment: TUDOR DOMAIN, RESIDUES 38-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q5T6S3
#2: Protein/peptide HISTONE H3


Mass: 1259.500 Da / Num. of mol.: 1 / Fragment: H3(31-41)K36ME3, RESIDUES 32-42 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE
121NOESY
131EDITED -FILTERED
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 200 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGERrefinement
NMRViewstructure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 10

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