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- PDB-2kwn: Solution structure of the double PHD (plant homeodomain) fingers ... -

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Basic information

Entry
Database: PDB / ID: 2kwn
TitleSolution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing acetylation at Lysine 16
Components
  • Histone peptide
  • Zinc finger protein DPF3
KeywordsMETAL BINDING PROTEIN / acetyl-lysine / Transcription regulation / Nucleus
Function / homology
Function and homology information


nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / muscle organ development / regulation of G1/S transition of mitotic cell cycle ...nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / muscle organ development / regulation of G1/S transition of mitotic cell cycle / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / positive regulation of myoblast differentiation / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / positive regulation of cell differentiation / nervous system development / chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / zinc ion binding / nucleoplasm / metal ion binding
Similarity search - Function
DPF1-3, N-terminal domain / : / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal ...DPF1-3, N-terminal domain / : / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Arachidonate 15-lipoxygenase / Zinc finger protein DPF3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
Model detailslowest energy, model 20
AuthorsZeng, L. / Zhang, Q. / Li, S. / Plotnikov, A.N. / Walsh, M.J. / Zhou, M.
CitationJournal: Nature / Year: 2010
Title: Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.
Authors: Zeng, L. / Zhang, Q. / Li, S. / Plotnikov, A.N. / Walsh, M.J. / Zhou, M.M.
History
DepositionApr 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
B: Histone peptide
A: Zinc finger protein DPF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6896
Polymers14,4282
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
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/peptide Histone peptide


Mass: 1681.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: P62805*PLUS
#2: Protein Zinc finger protein DPF3 / Zinc finger protein cer-d4 / BRG1-associated factor 45C / BAF45C


Mass: 12746.472 Da / Num. of mol.: 1 / Fragment: PHD-types 1 and 2 residues 261-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF3, BAF45C, CERD4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92784
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HN(CA)CB
1223D HN(COCA)CB
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D 13C-Edited 13C/15N-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1100 mM sodium phosphate, 2 mM DTT, 100% D2O100% D2O
2100 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMsodium phosphate-11
2 mMDTT-21
100 mMsodium phosphate-32
2 mMDTT-42
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003
Bruker DRXBrukerDRX5004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRView5.04Johnson, One Moon Scientificdata analysis
NMRView5.04Johnson, One Moon Scientificpeak picking
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle 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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