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- PDB-5tbn: Solution NMR structure of PHF20 PHD domain in complex with a hist... -

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Basic information

Entry
Database: PDB / ID: 5tbn
TitleSolution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide
Components
  • Histone H3.1
  • PHD finger protein 20
KeywordsTRANSCRIPTION / STRUCTURAL PROTEIN / PHD finger / Methylated lysine / TRANSCRIPTION - STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / epigenetic regulation of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Stabilization of p53 / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / nucleosome assembly / structural constituent of chromatin / Regulation of TP53 Degradation / nucleosome / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / nuclear membrane / gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / metal ion binding / cytosol
Similarity search - Function
PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Zinc finger, FYVE/PHD-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / PHD finger protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCui, G. / Botuyan, M.V. / Mer, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
CitationJournal: Cell Rep / Year: 2016
Title: PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation.
Authors: Klein, B.J. / Wang, X. / Cui, G. / Yuan, C. / Botuyan, M.V. / Lin, K. / Lu, Y. / Wang, X. / Zhao, Y. / Bruns, C.J. / Mer, G. / Shi, X. / Kutateladze, T.G.
History
DepositionSep 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 20
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2424
Polymers8,1112
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area5280 Å2
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 20 / Glioma-expressed antigen 2 / Hepatocellular carcinoma-associated antigen 58 / Novel zinc finger ...Glioma-expressed antigen 2 / Hepatocellular carcinoma-associated antigen 58 / Novel zinc finger protein / Transcription factor TZP


Mass: 6834.700 Da / Num. of mol.: 1 / Fragment: residues 646-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20, C20orf104, GLEA2, HCA58, NZF, TZP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BVI0
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1276.490 Da / Num. of mol.: 1 / Fragment: residues 2-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
132isotropic12D 1H-13C HSQC
142isotropic13D HN(CA)CB
152isotropic13D CBCA(CO)NH
162isotropic13D HNCO
172isotropic13D NH(CA)CO
182isotropic13D HBHA(CO)NH
192isotropic13D CCH-TOCSY
1102isotropic13D 1H-15N NOESY
1112isotropic13D 1H-13C NOESY aliphatic
1122isotropic13D 1H-13C NOESY aromatic
1132isotropic13D 13C,15N-filtered, 13C/15N-edited NOESY
1143isotropic12D 1H-13C HSQC
1153isotropic12D 1H-1H NOESY
1163isotropic12D 1H-1H COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.5 mM [U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution32 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2ONatural_abundance90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMPHF20 PHD domain[U-15N]1
6.0 mMH3K4me2 peptidenatural abundance1
25 mMsodium phosphatenatural abundance1
0.3 mMDSSnatural abundance1
1.5 mMsodium azidenatural abundance1
1.5 mMPHF20 PHD domain[U-13C; U-15N]2
6.0 mMH3K4me2 peptidenatural abundance2
25 mMsodium phosphatenatural abundance2
0.3 mMDSSnatural abundance2
1.5 mMsodium azidenatural abundance2
2 mMH3K4me2 peptidenatural abundance3
25 mMsodium phosphatenatural abundance3
0.3 mMDSSnatural abundance3
1.5 mMsodium azidenatural abundance3
Sample conditionsIonic strength: 20 mM sodium phosphate mM / Label: conditions_1 / pH: 7 / PH err: 0.2 / Pressure: 101325 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz / Details: Cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 9
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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