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- PDB-9qlm: Solution structure of the TAF3-PHD bound to a H3K4me3Q5ser histon... -

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Basic information

Entry
Database: PDB / ID: 9qlm
TitleSolution structure of the TAF3-PHD bound to a H3K4me3Q5ser histone tail peptide with a serotonylated glutamine
Components
  • Histone H3.1
  • Transcription initiation factor TFIID subunit 3
KeywordsGENE REGULATION / serotonylation / methylation / histone H3 / TFIID
Function / homology
Function and homology information


RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / maintenance of protein location in nucleus / histone H3K4me3 reader activity / transcription factor TFIID complex / negative regulation of signal transduction by p53 class mediator ...RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / maintenance of protein location in nucleus / histone H3K4me3 reader activity / transcription factor TFIID complex / negative regulation of signal transduction by p53 class mediator / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / 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 / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / male germ cell nucleus / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / mRNA transcription by RNA polymerase II / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / p53 binding / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / nuclear membrane / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / transcription by RNA polymerase II / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger ...Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
SEROTONIN / Histone H3.1 / Transcription initiation factor TFIID subunit 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Authorsvan Ingen, H. / Gielingh, H. / Pulido-Cortes, L. / Thijssen, V. / Timmers, H.T.M. / Jongkees, S. / Honorato, R.V. / Bonvin, A.M.J.J. / Liu, M. / Yoshisada, R. / Soares, L.R.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
iNEXT-DiscoveryPID 12004European Union
German Research Foundation (DFG)SFB992 Germany
German Research Foundation (DFG)TI688/1-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Molecular determinants for recognition of serotonylated chromatin.
Authors: Pulido-Cortes, L. / Gielingh, H. / Thijssen, V. / Liu, M. / Yoshisada, R. / Romao Soares, L. / Nizamuddin, S. / Friedrich, F. / Greschik, H. / Peng, L. / Vargas Honorato, R. / Jung, M. / ...Authors: Pulido-Cortes, L. / Gielingh, H. / Thijssen, V. / Liu, M. / Yoshisada, R. / Romao Soares, L. / Nizamuddin, S. / Friedrich, F. / Greschik, H. / Peng, L. / Vargas Honorato, R. / Jung, M. / Bonvin, A.M.J.J. / Biniossek, M.L. / Schule, R. / Jongkees, S. / van Ingen, H. / Timmers, H.T.M.
History
DepositionMar 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 3
B: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2715
Polymers9,9632
Non-polymers3073
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
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 Transcription initiation factor TFIID subunit 3 / 140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription ...140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / TAF(II)140 / TAF140 / TAFII-140 / TAFII140


Mass: 8611.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Plant Homeodomain of TAF3 with 2 zinc ions bound / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Taf3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HZG4
#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: 1351.553 Da / Num. of mol.: 1 / 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: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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
112isotropic12D F2-filtered NOESY
122isotropic12D F2-filtered TOCSY
132isotropic13D 1H-13C NOESY aliphatic
142isotropic13D 1H-13C NOESY aromatic
152isotropic13D 1H-15N NOESY
162isotropic12D 1H-13C HSQC
172isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.88 mM [U-13C; U-15N] TAF3-PHD, 0.88 mM H3K4me3Q5ser, 20 mM potassium phosphate, 4 mM potassium chloride, 10 uM zinc chloride, 0.01 % w/v sodium azide, 90% H2O/10% D2O
Details: 1:1 mix of TAF3-PHD (U-13C,15N) and unlabeled H3K4me3Q5ser peptide
Label: NOESY_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.88 mMTAF3-PHD[U-13C; U-15N]2
0.88 mMH3K4me3Q5sernatural abundance2
20 mMpotassium phosphatenatural abundance2
4 mMpotassium chloridenatural abundance2
10 uMzinc chloridenatural abundance2
0.01 % w/vsodium azidenatural abundance2
Sample conditionsDetails: low-salt and 293K for best quality filtered NOESY / Ionic strength: 44 mM / Label: NOESY_conditions / pH: 7 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKBonvinrefinement
HADDOCKBonvinstructure calculation
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leechemical shift assignment
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
RefinementMethod: molecular 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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