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- PDB-2lrq: Chemical Shift Assignment and Solution Structure of Fr822A from D... -

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Basic information

Entry
Database: PDB / ID: 2lrq
TitleChemical Shift Assignment and Solution Structure of Fr822A from Drosophila melanogaster. Northeast Structural Genomics Consortium Target Fr822A
ComponentsNuA4 complex subunit EAF3 homolog
KeywordsTRANSCRIPTION / Epigenetics / Lid Complex / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes / CEBS
Function / homology
Function and homology information


: / : / : / : / : / heterochromatin formation => GO:0031507 / : / chromosome separation / histone methyltransferase complex / NuA4 histone acetyltransferase complex ...: / : / : / : / : / heterochromatin formation => GO:0031507 / : / chromosome separation / histone methyltransferase complex / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / chromosome organization / enzyme regulator activity / methylated histone binding / DNA repair / chromatin binding / positive regulation of gene expression / 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
NuA4 complex subunit EAF3 homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsLee, H. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J.K. / Montelione, G. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG) / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS)
CitationJournal: To be Published
Title: Solution Structure of Fr822A from Drosophila melanogaster.
Authors: Lee, H.
History
DepositionApr 11, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NuA4 complex subunit EAF3 homolog


Theoretical massNumber of molelcules
Total (without water)10,0251
Polymers10,0251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein NuA4 complex subunit EAF3 homolog / Protein MRG15


Mass: 10025.209 Da / Num. of mol.: 1 / Fragment: UNP residues 11-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: MRG15, CG6363 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y0I1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The oligomeric states of the Fr822A were verified by correlation time measurements and concentration dependent studies. The results indicated that the Fr822A self-associates weakly at ...Details: The oligomeric states of the Fr822A were verified by correlation time measurements and concentration dependent studies. The results indicated that the Fr822A self-associates weakly at protein concentration below 1 mM. Using the residual dipolar couplings as well as chemical shift perturbations on dilution, we constructed dimeric models for Fr822A. Possible inter-subunit NOEs were identified based on these models. In cases where corresponding NOEs were ambiguous with intra-molecular NOEs, they were eliminated as constraints and the protein structure recalculated. The absence of structural variation and the failure to observed other predicted inter-subunit NOEs validated use of all NOEs as intra-subunit constraints.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11412D 1H-15N NH-J-Modulation-HSQC
11522D 1H-15N NH-J-Modulation-HSQC
11632D 1H-15N NH-J-Modulation-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] Fr822A, 20 mM sodium phosphate, 200 mM sodium chloride, 5 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
20.9 mM [U-100% 15N] Fr822A, 20 mM sodium phosphate, 200 mM sodium chloride, 12 mg Pf1 phage, 5 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
30.9 mM [U-100% 15N] Fr822A, 20 mM sodium phosphate, 200 mM sodium chloride, 4.2 % C12E5, 5 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMFr822A-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
200 mMsodium chloride-31
5 mMDTT-41
0.9 mMFr822A-5[U-100% 15N]2
20 mMsodium phosphate-62
200 mMsodium chloride-72
12 mg/mLPf1 phage-82
5 mMDTT-92
0.9 mMFr822A-10[U-100% 15N]3
20 mMsodium phosphate-113
200 mMsodium chloride-123
4.2 %C12E5-133
5 mMDTT-143
Sample conditionsIonic strength: 200 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.14Goddardchemical shift assignment
Sparky3.14Goddarddata analysis
VnmrJ2.1BVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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