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- PDB-6o22: Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine ace... -

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Basic information

Entry
Database: PDB / ID: 6o22
TitleStructure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate.
Components
  • Histone H3.2
  • Histone H4
  • Histone acetyltransferase RTT109
  • Histone chaperone ASF1
  • Vacuolar protein sorting-associated protein 75
KeywordsCHAPERONE
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 / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / protein transport / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / chromosome, telomeric region / protein heterodimerization activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily ...Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Histone chaperone ASF1 / Vacuolar protein sorting-associated protein 75 / Histone H4 / Histone H3.2 / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsDanilenko, N. / Carlomagno, T. / Kirkpatrick, J.P.
CitationJournal: Nat Commun / Year: 2019
Title: Histone chaperone exploits intrinsic disorder to switch acetylation specificity.
Authors: Nataliya Danilenko / Lukas Lercher / John Kirkpatrick / Frank Gabel / Luca Codutti / Teresa Carlomagno /
Abstract: Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both ...Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75
C: Histone acetyltransferase RTT109
D: Histone chaperone ASF1
E: Histone H3.2
F: Histone H4


Theoretical massNumber of molelcules
Total (without water)170,4786
Polymers170,4786
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18410 Å2
ΔGint-102 kcal/mol
Surface area57190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 150structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Vacuolar protein sorting-associated protein 75


Mass: 30656.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VPS75, YNL246W, N0890 / Production host: Escherichia coli (E. coli) / References: UniProt: P53853
#2: Protein Histone acetyltransferase RTT109 / Regulator of Ty1 transposition protein 109


Mass: 50765.434 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: RTT109, KIM2, REM50, YLL002W, L1377 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07794, histone acetyltransferase
#3: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 31585.139 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P32447
#4: Protein Histone H3.2 / Histone H3


Mass: 15421.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#5: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
122isotropic12D 1H-13C HSQC
133isotropic12D 1H-13C HSQC
144isotropic12D 1H-13C HSQC
155isotropic12D 1H-13C HSQC
166isotropic12D 1H-13C HSQC
177isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution170 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4, 100% D2OVps75_in_FC_ILV100% D2O
solution270 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag, 70 uM H4, 100% D2Ocomplex_Vps75(ILV)_H3(63C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution390 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 90 uM Rtt109, 90 uM Asf1, 90 uM H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag, 90 uM H4, 100% D2Ocomplex_Vps75(ILV)_H3(76C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution430 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(30C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(30C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(30C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution570 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4(82C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(82C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(82C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C) states.
solution680 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 80 uM Rtt109, 80 uM Asf1, 80 uM H3, 80 uM H4(45C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(45C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(45C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C)
solution730 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(93C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2Ocomplex_Vps75(ILV)_H4(93C)-tag100% D2OPRE experiment on the full Rtt109-Vps75(2)-Asf1-H3:H4 complex reconsituted with perdeuterated ILV-labelled Vps75 and H4(93C) mutant with a cysteine coupled to a paramagnetic tag. The spectra were recorded in paramagnetic and diamagnetic (after addition of vit.C)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
70 uMVps75 (dimer)ILV methyl labelled, perdeuterated1
70 uMRtt109natural abundance1
70 uMAsf1natural abundance1
70 uMH3natural abundance1
70 uMH4natural abundance1
70 uMVps75 (dimer)ILV methyl labelled, perdeuterated2
70 uMRtt109natural abundance2
70 uMAsf1natural abundance2
70 uMH3(110A,63C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance2
70 uMH4natural abundance2
90 uMVps75 (dimer)ILV methyl labelled, perdeuterated3
90 uMRtt109natural abundance3
90 uMAsf1natural abundance3
90 uMH3(110A,76C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance3
90 uMH4natural abundance3
30 uMVps75 (dimer)ILV methyl labelled, perdeuterated4
30 uMRtt109natural abundance4
30 uMAsf1natural abundance4
30 uMH3natural abundance4
30 uMH4(30C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance4
70 uMVps75 (dimer)ILV methyl labelled, perdeuterated5
70 uMRtt109natural abundance5
70 uMAsf1natural abundance5
70 uMH3natural abundance5
70 uMH4(82C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance5
80 uMVps75 (dimer)ILV methyl labelled, perdeuterated6
80 uMRtt109natural abundance6
80 uMAsf1natural abundance6
80 uMH3natural abundance6
80 uMH4(45C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance6
30 uMVps75 (dimer)ILV methyl labelled, perdeuterated7
30 uMRtt109natural abundance7
30 uMAsf1natural abundance7
30 uMH3natural abundance7
30 uMH4(93C) mutant with a cysteine coupled to a paramagnetic tagnatural abundance7
Sample conditionsIonic strength: 150 mM / Label: cond_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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Data collection

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz
Soln scatter

Buffer name: 50 MM CITRATE, 150 MM NACL, 5MM BME IN 99.9% D2O / Data analysis software list: PRIMUS, GNOM / Sample pH: 6.5 / Source class: N / Temperature: 298 K / Type: neutron

IDConc. range (mg/ml)Data reduction software listDetector typeMean guiner radius (nm)Mean guiner radius esd (nm)Protein lengthSource beamline instrumentSource type
14.9ILL IN-HOUSE PACKAGE (GRASP)He multidetector 128 linear sensitive Reuter-Stokes detector2.840.0189.5D22ILL
22.35QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.530.03811.5KWS-1FRM2
33.85QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detectorKWS-1FRM2
43.8QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.280.04610.5KWS-1FRM2
54.7QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.50.04611KWS-1FRM2
65.2QTIKWS6Li-Scintillator 1 mm thickness + photomultiplier detector3.060.07610.5KWS-1FRM2

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Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNdata analysis
HADDOCKBonvinstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
FuDAD. Flemming Hansendata analysis
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 1
Soln scatter modelMethod: X-RAY STRUCTURES OF THE SUBUNITS WERE DOCKED WITH HADDOCK-BASED M3 DOCKING PROTOCOL. DOCKING WAS GUIDED BY PRE DISTANCE RESTRAINTS, STRUCTURES WERE SELECTED BY FITNESS TO THE SANS DATA.
Conformer selection criteria: BEST FITNESS TO THE SANS DATA, CLOSEST TO THE CLUSTER CENTER.
Details: THE STRUCTURE WAS DETERMINED USING A HADDOCK-BASED M3 DOCKING PROTOCOL. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ID 3Q66, PDB ID 2HUE. PRE DISTANCE RESTRAINTS WERE ...Details: THE STRUCTURE WAS DETERMINED USING A HADDOCK-BASED M3 DOCKING PROTOCOL. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ID 3Q66, PDB ID 2HUE. PRE DISTANCE RESTRAINTS WERE USED FOR STRUCTURE CALCULATION WITH HADDOCK-M3. 5000 STRUCTURES WERE CALCULATED DURING THE IT0 STAGE, 150 STRUCTURES WERE CALCULATED DURING THE IT1 STAGE. SANS DATA WERE USED FOR THE STRUCTURE SELECTION.
Entry fitting list: PDB ID 3Q66, PDB ID 2HUE / Num. of conformers calculated: 150 / Num. of conformers submitted: 1 / Software author list: KARACA, CARLOMAGNO, RODRIGUES, BONVIN / Software list: M3

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