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- PDB-2bud: The solution structure of the chromo barrel domain from the males... -

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Basic information

Entry
Database: PDB / ID: 2bud
TitleThe solution structure of the chromo barrel domain from the males- absent on the first (MOF) protein
ComponentsMALES-ABSENT ON THE FIRST PROTEIN
KeywordsTRANSFERASE / MOF / HAT / ACETYL-TRANSFER / DOSAGE COMPENSATION COMPLEX / DCC / ROYAL FAMILY / CHROMODOMAIN LIKE / BETA BARREL / TRANSFERASE ACYLTRANSFERASE / METAL-BINDING
Function / homology
Function and homology information


polytene chromosome interband / positive regulation of gene expression, epigenetic / Formation of WDR5-containing histone-modifying complexes / X chromosome located dosage compensation complex, transcription activating / HATs acetylate histones / MSL complex / dosage compensation by hyperactivation of X chromosome / sex-chromosome dosage compensation / NSL complex / nuclear chromosome ...polytene chromosome interband / positive regulation of gene expression, epigenetic / Formation of WDR5-containing histone-modifying complexes / X chromosome located dosage compensation complex, transcription activating / HATs acetylate histones / MSL complex / dosage compensation by hyperactivation of X chromosome / sex-chromosome dosage compensation / NSL complex / nuclear chromosome / lncRNA binding / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / X chromosome / histone acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / DNA damage response, signal transduction by p53 class mediator / transcription regulator complex / chromatin binding / positive regulation of DNA-templated transcription / zinc ion binding / nucleus
Similarity search - Function
: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo-like domain superfamily ...: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / SH3 type barrels. / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone acetyltransferase MOF
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / ARIA
AuthorsNielsen, P.R. / Nietlispach, D. / Buscaino, A. / Warner, R.J. / Akhtar, A. / Murzin, A.G. / Murzina, N.V. / Laue, E.D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of the Chromo Barrel Domain from the Mof Acetyltransferase
Authors: Nielsen, P.R. / Nietlispach, D. / Buscaino, A. / Warner, R.J. / Akhtar, A. / Murzin, A.G. / Murzina, N.V. / Laue, E.D.
History
DepositionJun 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALES-ABSENT ON THE FIRST PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,3521
Polymers10,3521
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)25 / 100structures with the lowest energy
RepresentativeModel #4

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Components

#1: Protein MALES-ABSENT ON THE FIRST PROTEIN / PUTATIVE ACETYL TRANSFERASE MOF


Mass: 10352.486 Da / Num. of mol.: 1 / Fragment: CHROMO BARREL DOMAIN, RESIDUES 367-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): TUNER(DE3) PLACI / References: UniProt: O02193, histone acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY AND TOCSY
1213D 13C-SEPARATED NOESY-HSQC
1313D (H)CCH-TOCSY
1413D TROSY-HNCO
2513D INTRAHNCA
2613D HNCO
2713D HN(CA)CB
2813D CBCA(CO)NH
2913D (H)CC(CO)NH
21013D (H)CC(CO)NH
21113D (H)CCH-TOCSY
21214D 13C
213115N- SEPARATED HMQC-NOESY-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USIGN TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELLED MOF CHROMO BARREL DOMAIN. PHI, PSI AND CHI1 ANGLES WERE DETERMINED FROM 3J ( HA,HB),(HN,HA),(CO,CO) AND ...Text: THE STRUCTURE WAS DETERMINED USIGN TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELLED MOF CHROMO BARREL DOMAIN. PHI, PSI AND CHI1 ANGLES WERE DETERMINED FROM 3J ( HA,HB),(HN,HA),(CO,CO) AND (N,CG) COUPLINGS AND DIPOLAR- DIPOLAR AND DIPOLAR-CHEMICAL SHIFT ANISOTROPY RELAXATION INTERFERENCE.

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Sample preparation

DetailsContents: 90% WATER/10% D2O, 25MMOLES/L SODIUM PHOSPHATE, 150MMOL/L SODIUM CHLORIDE
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1212 mM51.0 atm298.0 K
2212 mM51.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS 1.0 WITH ARIA1.1.2 ARIA1.1.2ARIA1.1.2A.T.BRUNGER,J.P.LINGE,S.J.ODONOGHUE,M.NILGES.refinement
ARIAstructure solution
CNSstructure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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