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- PDB-2mum: Solution structure of the PHD domain of Yeast YNG2 -

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Basic information

Entry
Database: PDB / ID: 2mum
TitleSolution structure of the PHD domain of Yeast YNG2
ComponentsChromatin modification-related protein YNG2
KeywordsTranscription Regulator / PHD finger
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / piccolo histone acetyltransferase complex / SUMOylation of transcription cofactors / NuA4 histone acetyltransferase complex / methylated histone binding / meiotic cell cycle / nucleosome / chromatin remodeling / DNA repair / DNA-templated transcription ...PI5P Regulates TP53 Acetylation / piccolo histone acetyltransferase complex / SUMOylation of transcription cofactors / NuA4 histone acetyltransferase complex / methylated histone binding / meiotic cell cycle / nucleosome / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / metal ion binding / nucleus / cytosol
Similarity search - Function
Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / 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. ...Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / 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 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromatin modification-related protein YNG2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsTaeb, S. / Kaustov, L. / Lemak, A. / Farhadi, S. / Sheng, Y.
CitationJournal: To be Published
Title: Solution structure of the PHD domain of Yeast YNG2
Authors: Taeb, S. / Kaustov, L. / Lemak, A. / Farhadi, S. / Sheng, Y.
History
DepositionSep 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: 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_conn_angle / struct_conn / 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 / _pdbx_nmr_software.name / _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.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.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_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
A: Chromatin modification-related protein YNG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0703
Polymers5,9391
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 #1lowest energy

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Components

#1: Protein/peptide Chromatin modification-related protein YNG2 / ESA1-associated factor 4 / ING1 homolog 2


Mass: 5938.829 Da / Num. of mol.: 1 / Fragment: PHD-type domain residues 222-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: YNG2, EAF4, NBN1, YHR090C / Production host: Escherichia coli (E. coli) / References: UniProt: P38806
#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
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNCA
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D HNCO
1912D 1H-15N HSQC
11012D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein, 300 mM sodium chloride, 2.7 mM potassium chloride, 2 mM potassium phosphate, 10 mM sodium phosphate, 0.05 mM CHAPS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1-1[U-13C; U-15N]1
300 mMsodium chloride-21
2.7 mMpotassium chloride-31
2 mMpotassium phosphate-41
10 mMsodium phosphate-51
0.05 mMCHAPS-61
Sample conditionsIonic strength: 300 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCGUILemak A., Gutmanas A., Chitayat S., Karra M., Far s C., Sunnerhagen M., and Arrowsmith C.H.chemical shift assignment
FMCGUILemak A., Gutmanas A., Chitayat S., Karra M., Far s C., Sunnerhagen M., and Arrowsmith C.H.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
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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