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- PDB-7uqj: Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 h... -

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Basic information

Entry
Database: PDB / ID: 7uqj
TitleCryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS and histone H3 tail in state II
Components
  • ATPase histone chaperone YTA7
  • Histone H3
KeywordsTRANSFERASE / AAA+ ATPase / chromatin remodeler
Function / homology
Function and homology information


ATP-dependent histone chaperone activity / sexual sporulation resulting in formation of a cellular spore / positive regulation of invasive growth in response to glucose limitation / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / CENP-A containing chromatin assembly / replication fork protection complex / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I ...ATP-dependent histone chaperone activity / sexual sporulation resulting in formation of a cellular spore / positive regulation of invasive growth in response to glucose limitation / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / CENP-A containing chromatin assembly / replication fork protection complex / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / chromosome, centromeric region / CENP-A containing nucleosome / structural constituent of chromatin / nucleosome / chromosome / chromatin organization / histone binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / Histone H3 signature 1. / ATPase, AAA-type, core / Histone H3 signature 2. / Histone H3 ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / Histone H3 signature 1. / ATPase, AAA-type, core / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Bromodomain profile. / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATPase histone chaperone YTA7 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang, F. / Feng, X. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
CitationJournal: J Biol Chem / Year: 2023
Title: The Saccharomyces cerevisiae Yta7 ATPase hexamer contains a unique bromodomain tier that functions in nucleosome disassembly.
Authors: Feng Wang / Xiang Feng / Qing He / Hua Li / Huilin Li /
Abstract: The Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to ...The Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to promote nucleosome disassembly for DNA replication or RNA transcription. By cryo-EM analysis, here we show that Yta7 assembles a three-tiered hexamer with a top BRD tier, a middle AAA1 tier, and a bottom AAA2 tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix, termed BRD-interacting motif (BIM), of the largely disordered N-terminal region. The BIM motif is unique to the baker's yeast, and we show both BRD and BIM contribute to nucleosome recognition. We found that Yta7 binds both acetylated and nonacetylated H3 peptides but with a higher affinity for the unmodified peptide. This property is consistent with the absence of key residues of canonical BRDs involved in acetylated peptide recognition and the role of Yta7 in general nucleosome remodeling. Interestingly, the BRD tier exists in a spiral and a flat-ring form on top of the Yta7 AAA+ hexamer. The spiral is likely in a nucleosome-searching mode because the bottom BRD blocks the entry to the AAA+ chamber. The flat ring may be in a nucleosome disassembly state because the entry is unblocked and the H3 peptide has entered the AAA+ chamber and is stabilized by the AAA1 pore loops 1 and 2. Indeed, we show that the BRD tier is a flat ring when bound to the nucleosome. Overall, our study sheds light on the nucleosome disassembly by Yta7.
History
DepositionApr 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase histone chaperone YTA7
B: ATPase histone chaperone YTA7
C: ATPase histone chaperone YTA7
D: ATPase histone chaperone YTA7
E: ATPase histone chaperone YTA7
F: ATPase histone chaperone YTA7
G: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)978,91917
Polymers975,7787
Non-polymers3,14110
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ATPase histone chaperone YTA7 / ATPase family AAA domain-containing protein YTA7 / AAA-ATPase / Tat-binding homolog 7


Mass: 162182.969 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YTA7, YGR270W / Plasmid: Yeast integrative vector pBS43
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40340, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide Histone H3 /


Mass: 2680.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61830
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Yta7 with H3N tail / Type: COMPLEX
Details: The translocation state of Histone 3 N-terminal peptide by Yta7
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.93 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Plasmid: Yeast integrative vector pBS43
Buffer solutionpH: 7.6
Details: Solution was made fresh and detergent was added to solve preference orientation issue.
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMpotassium chlorideKCl1
225 mMHEPES-Potassium hydroxide1
31 mMEthylenediaminetetraacetic acid1
44 mMMagnesium chlorideMgCl21
52 mM2-mercaptoethanol2-me1
62 mMATPgS1
70.025 v/voctyl D-glucosideOctyl_glucoside1
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was a novel chromatin remodeler and a AAA+ ATPase.
Specimen supportDetails: The grids were doulbe blots / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: Blot 3S, blot forth 3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 193 K / Temperature (min): 193 K
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Details: A total of 75 frames were recorded for each micrograph stack.

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Processing

EM software
IDNameVersionCategoryDetails
2RELION3.1image acquisition
3cryoSPARC3.2.0image acquisitiononly use for 2D classfication
5CTFFIND1.4.10CTF correction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 431065 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient

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