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- PDB-2k3x: Solution structure of EAF3 chromo barrel domain -

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Basic information

Entry
Database: PDB / ID: 2k3x
TitleSolution structure of EAF3 chromo barrel domain
ComponentsChromatin modification-related protein EAF3
KeywordsTRANSCRIPTION REGULATOR / Eaf3 / Chromo barrel domain / Histone deacetylase / methylated histones H3K36 and H3K4 / Chromatin regulator / DNA damage / DNA repair / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / nucleosome assembly / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain ...MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chromatin modification-related protein EAF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMer, G. / Xu, C.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for the Recognition of Methylated Histone H3K36 by the Eaf3 Subunit of Histone Deacetylase Complex Rpd3S.
Authors: Xu, C. / Cui, G. / Botuyan, M.V. / Mer, G.
History
DepositionMay 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromatin modification-related protein EAF3


Theoretical massNumber of molelcules
Total (without water)14,1041
Polymers14,1041
Non-polymers00
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromatin modification-related protein EAF3 / ESA1-associated factor 3


Mass: 14103.966 Da / Num. of mol.: 1 / Fragment: UNP residues 1 to 113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EAF3, YPR023C, YP9367.03C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12432
Nonpolymer detailsHIS RESIDUES HAVE HYDROGENS ONLY ON THE EPSILON NITROGEN

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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-15N HSQC
1322D 1H-13C HSQC
1413D 1H-15N TOCSY
1513D 1H-15N NOESY
1623D HN(CA)CB
1723D CBCA(CO)NH
1823D HBHA(CO)NH
1923D (H)CCH-TOCSY
11023D HNCO
11123D HCACO
11223D CCH-COSY
11323D CCH-TOCSY
11423D C(CO)NH
11523D H(CCO)NH
11622D HBCGCDCEHE
11722D HBCGCDHD
11823D 1H-13C NOESY
11923D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-1.5 mM [U-100% 15N] Eaf3, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 800 mM urea, 93% H2O/7% D2O93% H2O/7% D2O
20.4-1.5 mM [U-100% 13C; U-100% 15N] Eaf3, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 800 mM urea, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMEaf3[U-100% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
1 mMEDTA1
2 mMDTT1
800 mMurea1
0.4 mMEaf3[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
1 mMEDTA2
2 mMDTT2
800 mMurea2
Sample conditionsIonic strength: 50 / pH: 6.7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
SparkyGoddarddata analysis
SANEDuggan, Legge, Dyson & Wrightdata analysis
RefinementMethod: simulated annealing / 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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