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- PDB-2k17: Solution structure of the TAF3 PHD domain in complex with a H3K4m... -

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Basic information

Entry
Database: PDB / ID: 2k17
TitleSolution structure of the TAF3 PHD domain in complex with a H3K4me3 peptide
Components
  • H3K4me3 peptide
  • Transcription initiation factor TFIID subunit 3
KeywordsTRANSCRIPTION / PROTEIN / Alternative splicing / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc / Zinc-finger
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 / transcription regulator inhibitor activity / transcription factor TFIID complex / positive regulation of transcription initiation by RNA polymerase II ...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 / transcription regulator inhibitor activity / transcription factor TFIID complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / male germ cell nucleus / mRNA transcription by RNA polymerase II / negative regulation of DNA-binding transcription factor activity / p53 binding / nuclear membrane / transcription by RNA polymerase II / protein heterodimerization activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailssolution structure of the planhomeodomain of TFIID sununit TAF3 with a peptide derived from the N ...solution structure of the planhomeodomain of TFIID sununit TAF3 with a peptide derived from the N terminal tail of histone H3 trimethylated at K4
Authorsvan Ingen, H. / van Schaik, F.M.A. / Wienk, H. / Timmers, M. / Boelens, R.
CitationJournal: To be Published
Title: Recognition of the H3K4me3 mark by the TAF3-PHD finger
Authors: van Ingen, H. / van Schaik, F.M.A. / Wienk, H. / Ballering, J. / Deschesne, A. / Kruijzer, J. / Timmers, H. / Boelens, R.
History
DepositionFeb 22, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: 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 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: H3K4me3 peptide
A: Transcription initiation factor TFIID subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1504
Polymers10,0202
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide H3K4me3 peptide


Mass: 1407.620 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Transcription initiation factor TFIID subunit 3 / TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / 140 kDa TATA box- ...TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / 140 kDa TATA box-binding protein-associated factor / TAF140 / TAFII140


Mass: 8611.936 Da / Num. of mol.: 1 / Fragment: planthomeodomain finger
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Taf3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5HZG4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: solution structure of the planhomeodomain of TFIID sununit TAF3 with a peptide derived from the N terminal tail of histone H3 trimethylated at K4
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.4 mM [U-13C; U-15N] TAF3_PHD, 150 mM potassium chloride, 20 mM potassium phosphate, 0.01 mM ZnCl2, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMTAF3_PHD[U-13C; U-15N]1
150 mMpotassium chloride1
20 mMpotassium phosphate1
0.01 mMZnCl21
Sample conditionspH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: refinement in explicit solvent using RECOORD protocol
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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