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- PDB-2jmi: NMR solution structure of PHD finger fragment of Yeast Yng1 prote... -

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Basic information

Entry
Database: PDB / ID: 2jmi
TitleNMR solution structure of PHD finger fragment of Yeast Yng1 protein in free state
ComponentsProtein YNG1
KeywordsPROTEIN BINDING / PHD / Histone / Recognition / Yeast
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / SUMOylation of transcription cofactors / histone acetyltransferase complex / methylated histone binding / positive regulation of transcription elongation by RNA polymerase II / chromatin organization / chromatin remodeling / DNA-templated transcription ...PI5P Regulates TP53 Acetylation / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / SUMOylation of transcription cofactors / histone acetyltransferase complex / methylated histone binding / positive regulation of transcription elongation by RNA polymerase II / chromatin organization / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / metal ion binding / nucleus
Similarity search - Function
ING family / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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
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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4003
Polymers10,2701
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 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: 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
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HN(CO)CA
1813D HBHA(CO)NH
1933D (H)CCH-TOCSY
11023D 1H-15N NOESY
11133D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.54 mM [U-13C, U-15N] YNG1_PHD, 90% H2O, 10% D2O90% H2O/10% D2O
20.6 mM [U-15N] YNG1_PHD, 90% H2O, 10% D2O90% H2O/10% D2O
30.54 mM [U-13C, U-15N] YNG1_PHD, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.54 mMYNG1_PHD[U-13C; U-15N]1
0.6 mMYNG1_PHD[U-15N]2
0.54 mMYNG1_PHD[U-13C; U-15N]3
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
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CARAKeller and Wuthrichstructure solution
CARAKeller and Wuthrichdata analysis
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 least restraint violations
Conformers calculated total number: 85 / Conformers submitted total number: 20

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