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- PDB-6f0y: Rtt109 peptide bound to Asf1 -

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Basic information

Entry
Database: PDB / ID: 6f0y
TitleRtt109 peptide bound to Asf1
Components
  • Histone chaperone ASF1
  • histone acetyltransferase Rtt109 C-terminus
KeywordsTRANSFERASE / histone chaperone / acetyl transferase
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange / transposable element silencing / histone H3 acetyltransferase activity / DNA replication-dependent chromatin assembly / nucleosome disassembly ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange / transposable element silencing / histone H3 acetyltransferase activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / protein-lysine-acetyltransferase activity / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / 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 / positive regulation of transcription elongation by RNA polymerase II / protein modification process / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / chromosome, telomeric region / DNA damage response / regulation of transcription by RNA polymerase II / chromatin / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein ...Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone ASF1 / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics / molecular dynamics
AuthorsLercher, L. / Kirkpatrick, J.P. / Carlomagno, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Molecular Biology OrganizationALTF 1474-2014, Marie Curie Actions, LTFCOFUND2013, GA-2103-609409 Germany
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural characterization of the Asf1-Rtt109 interaction and its role in histone acetylation.
Authors: Lercher, L. / Danilenko, N. / Kirkpatrick, J. / Carlomagno, T.
History
DepositionNov 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.5May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.6May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone ASF1
B: histone acetyltransferase Rtt109 C-terminus


Theoretical massNumber of molelcules
Total (without water)21,0152
Polymers21,0152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1130 Å2
ΔGint-5 kcal/mol
Surface area10740 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 19327.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ASF1, CIA1, YJL115W, J0755 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32447
#2: Protein/peptide histone acetyltransferase Rtt109 C-terminus


Mass: 1687.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q07794*PLUS, histone acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D (H)CCH-TOCSY
131isotropic1(HB)CB(CGCD)HD
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY
161isotropic13D 13C,15N filtered 1H-13C NOESY
172isotropic12D 1H-15N HSQC
281anisotropic22D 1H-15N HSQC
191isotropic22D 1H-15N HSQC
2101anisotropic22D 1H-15N TROSY-HSQC
1111isotropic22D 1H-15N TROSY-HSQC
1123isotropic12D 1H-1H TOCSY
1133isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.5 mM [U-99% 13C; U-99% 15N] Histone chaperone Asf1, 3 mM histone acetyltransferase Rtt109 C-terminus, 90% H2O/10% D2OCNAsf1_Rtt10990% H2O/10% D2O
solution30.5 mM [U-99% 13C; U-99% 15N; U-99% 2D] Histone chaperone ASF1, 0.15 mM histone acetyltransferase Rtt109 C-terminus, 90% H2O/10% D2ODCNasf1_rttC90% H2O/10% D2O
solution20.15 mM [U-99% 13C; U-99% 15N] Histone chaperone Asf1, 0.5 mM histone acetyltransferase Rtt109 C-terminus, 100% D2Oh_exchange100% D2Oquickly buffer exchanged into 100% D2O buffer
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHistone chaperone Asf1[U-99% 13C; U-99% 15N]1
3 mMhistone acetyltransferase Rtt109 C-terminusnatural abundance1
0.5 mMHistone chaperone ASF1[U-99% 13C; U-99% 15N; U-99% 2D]3
0.15 mMhistone acetyltransferase Rtt109 C-terminusnatural abundance3
0.15 mMHistone chaperone Asf1[U-99% 13C; U-99% 15N]2
0.5 mMhistone acetyltransferase Rtt109 C-terminusnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
1150 mMconditions_16.2ambient Pa298 K
2150 mMphage6.2ambient Pa298 Kincluding Pf1 bacteriophage at 8.7 mg/mL, giving a residual 2H quadrupolar splitting of the HOD signal of 7.3 Hz

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD8501
Bruker AVANCE III HDBrukerAVANCE III HD6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.4.2CCPNpeak picking
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CNS1.21Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenstructure calculation
ARIA2.3W. Rieping, M. Habeck, B. Bardiaux, A. Bernard, T.E. Malliavin, M. Nilgesstructure calculation
PALESM. Zweckstetterdata analysis
TALOS-NY. Shen, A. Baxdata analysis
CNS1.21Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenstructure calculation
CNS1.21Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing3
torsion angle dynamics9
molecular dynamics10
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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