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- PDB-2fuu: NMR solution structure of the PHD domain from the human BPTF in c... -

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Basic information

Entry
Database: PDB / ID: 2fuu
TitleNMR solution structure of the PHD domain from the human BPTF in complex with H3(1-15)K4me3 peptide
Components
  • Histone H3
  • bromodomain PHD finger transcription factor
KeywordsPROTEIN BINDING / BPTF / NURF / PHD DOMAIN / HISTONE RECOGNITION / H3K4ME3
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / structural constituent of chromatin / nucleosome ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / structural constituent of chromatin / nucleosome / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / dendrite / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site ...Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / 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 / 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 / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Histone H3 / Nucleosome-remodeling factor subunit BPTF / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / The structure was solved using a torsion angle simulated annealing protocol
AuthorsIlin, S. / Patel, D.J.
CitationJournal: Nature / Year: 2006
Title: Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.
Authors: Li, H. / Ilin, S. / Wang, W. / Duncan, E.M. / Wysocka, J. / Allis, C.D. / Patel, D.J.
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: bromodomain PHD finger transcription factor
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7904
Polymers8,6592
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 85structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein bromodomain PHD finger transcription factor


Mass: 7050.871 Da / Num. of mol.: 1 / Fragment: PHD FINGER DOMAIN (RESIDUES 2583-2639)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGex6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta 2 / References: GenBank: 31322942, UniProt: Q12830*PLUS
#2: Protein/peptide Histone H3 /


Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: H3(1-15)K4me3 / Mutation: K4(M3L) / Source method: obtained synthetically
Details: Synthetic. The sequence ARTKQTARKSTGGKA occurs naturally in humans on Histone 3
References: UniProt: P61836, UniProt: Q7M3Z9*PLUS
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1323D filter-edit 15N-separated NOESY
1413D filter-edit 13C-separated NOESY
NMR detailsText: The structure was determined using various triple-resonance NMR experiments plus filter edit experiments to determine the structure of the peptide.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.64 mM PHD finger U-15N,13C; 3.0 mM H3(1-15)K4me3; 20 mM Phosphate buffer pH 7.5, 50 mM KCl, 5 mM DTT90% H2O/10% D2O
20.62 mM PHD finger U-15N, 3.0 mM H3(1-15)K4me3; 20 mM Phosphate buffer pH 7.5, 50 mM KCl, 5 mM DTT90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM KCl / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.5Brukercollection
VNMR1.6cVariancollection
CARA1.5.3Rochus Kellerdata analysis
X-PLOR2.13G. Marius Clorestructure solution
NMRPipeF. Delaglioprocessing
X-PLOR2.13G. Marius Clorerefinement
RefinementMethod: The structure was solved using a torsion angle simulated annealing protocol
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 85 / Conformers submitted total number: 20

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