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- PDB-2jmj: NMR solution structure of the PHD domain from the yeast YNG1 prot... -

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Basic information

Entry
Database: PDB / ID: 2jmj
TitleNMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide
Components
  • Histone H3
  • Protein YNG1
KeywordsPROTEIN BINDING / Histone / PHD / H3K4me3 / complex
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / SUMOylation of transcription cofactors / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I ...PI5P Regulates TP53 Acetylation / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / SUMOylation of transcription cofactors / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / histone acetyltransferase complex / CENP-A containing nucleosome / methylated histone binding / positive regulation of transcription elongation by RNA polymerase II / structural constituent of chromatin / nucleosome / chromatin organization / chromatin remodeling / protein heterodimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus
Similarity search - Function
ING family / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 ...ING family / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3 / Protein YNG1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsIlin, S. / Taverna, S.D. / Rogers, R.S. / Tanny, J.C. / Lavender, H. / Li, H. / Baker, L. / Boyle, J. / Blair, L.P. / Chait, B.T. ...Ilin, S. / Taverna, S.D. / Rogers, R.S. / Tanny, J.C. / Lavender, H. / Li, H. / Baker, L. / Boyle, J. / Blair, L.P. / Chait, B.T. / Patel, D.J. / Aitchison, J.D. / Tackett, A.J. / Allis, C.D.
CitationJournal: Mol.Cell / Year: 2006
Title: Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs
Authors: Taverna, S.D. / Ilin, S. / Rogers, R.S. / Tanny, J.C. / Lavender, H. / Li, H. / Baker, L. / Boyle, J. / Blair, L.P. / Chait, B.T. / Patel, D.J. / Aitchison, J.D. / Tackett, A.J. / Allis, C.D.
History
DepositionNov 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: 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_conn_type / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein YNG1
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5064
Polymers11,3752
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein YNG1 / ING1 homolog 1


Mass: 10269.640 Da / Num. of mol.: 1 / Fragment: PHD finger
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YNG1 / Plasmid: pGex-4T / Production host: Escherichia coli (E. coli) / References: UniProt: Q08465
#2: Protein/peptide Histone H3 /


Mass: 1105.334 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide H3(1-9)K4me3 is naturally found in Saccharomyces cerevisiae (LOCUS AAS64341 to AAS64341).
References: UniProt: P61830
#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
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-1H TOCSY filter
1422D 1H-1H NOESY filter
1523D HNCA
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11123D 1H-15N NOESY filter
11223D 1H-13C NOESY filter

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Sample preparation

Details
Solution-IDContentsSolvent system
10.52 mM [U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O90% H2O/10% D2O
20.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.52 mMYNG1_PHD[U-15N]1
2.5 mMH3(1-9)K4me31
2 mMDTT1
50 mMpotassium chloride1
20 mMsodium phosphate1
0.48 mMYNG1_PHD[U-13C; U-15N]2
2.5 mMH3(1-9)K4me32
2 mMDTT2
50 mMpotassium chloride2
20 mMsodium phosphate2
Sample conditionsIonic strength: 50 / pH: 7.5 / Pressure: ambient / Temperature: 20 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
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloredata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichsolution structure
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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