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- EMDB-26682: Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 h... -

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Basic information

Entry
Database: EMDB / ID: EMD-26682
TitleCryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS in state I
Map dataPrimary map
Sample
  • Complex: Complex of Yta7 and ATPgS (spiral BRD)
    • Protein or peptide: Yta7
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsWang F / Feng X / Li H
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26682.png

Downloads & links

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Map

FileDownload / File: emd_26682.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0083
Minimum - Maximum-0.014492278 - 1.9355737
Average (Standard dev.)0.0038814729 (±0.044885434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw map

Fileemd_26682_additional_1.map
AnnotationRaw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26682_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26682_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Yta7 and ATPgS (spiral BRD)

EntireName: Complex of Yta7 and ATPgS (spiral BRD)
Components
  • Complex: Complex of Yta7 and ATPgS (spiral BRD)
    • Protein or peptide: Yta7

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Supramolecule #1: Complex of Yta7 and ATPgS (spiral BRD)

SupramoleculeName: Complex of Yta7 and ATPgS (spiral BRD) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 930 KDa

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Macromolecule #1: Yta7

MacromoleculeName: Yta7 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: HHHHHHHHHH TSGSMDYKDH DGDYKDHDID YKDDDDKMAR NLRNRRGSDV EDASNAKVGY ETQIKDENGI IHTTTRSLRK INYAEIEKVF DFLEDDQVMD KDETPVDVTS DEHHNNNQKG DDEDDDVDLV SPHENARTNE ELTNERNLRK RKAHDPEEDD ESFHEEDVDD ...String:
HHHHHHHHHH TSGSMDYKDH DGDYKDHDID YKDDDDKMAR NLRNRRGSDV EDASNAKVGY ETQIKDENGI IHTTTRSLRK INYAEIEKVF DFLEDDQVMD KDETPVDVTS DEHHNNNQKG DDEDDDVDLV SPHENARTNE ELTNERNLRK RKAHDPEEDD ESFHEEDVDD DEEEEEADEF EDEYLDEDSK DNNRRRRAAD RKFVVPDPDD DEEYDEDDEE GDRISHSASS KRLKRANSRR TRSSRHPETP PPVRRALRSR TRHSRTSNEE NDDENDNSRN EALTLADEIR ELQEDSPIRE KRFLRERTKP VNYKLPPPLT ASNAEEFIDK NNNALSFHNP SPARRGRGGW NASQNSGPTR RLFPTGGPFG GNDVTTIFGK NTNFYNQVPS AFSDNNNNKL ILDSDSSDDE ILPLGVTPKT KKENTQKKKK KKPEIADLDP LGVDMNVNFD DIGGLDNYID QLKEMVALPL LYPELYQNFN ITPPRGVLFH GPPGTGKTLM ARALAASCSS DERKITFFMR KGADILSKWV GEAERQLRLL FEEAKKHQPS IIFFDEIDGL APVRSSKQEQ IHASIVSTLL ALMDGMDNRG QVIVIGATNR PDAVDPALRR PGRFDREFYF PLPDVKARFK ILQIQTRKWS SPLSTNFIDK LAFLTKGYGG ADLRSLCTEA ALISIQRSFP QIYRSNDKLL VDPSKIKVKV SDFMLALKKI VPSSARSTGS SPQPLPELIK PLLADQLNNL KNKLDYMLNI KDTTFQRNTS LLQNFIDYEE YSGEEEEHDK YGGNEDTSSF RSYEFFESMA ESQICKPRLL INGPKGNGQQ YVGAAILNYL EEFNVQNLDL ASLVSESSRT IEAAVVQSFM EAKKRQPSVV FIPNLDIWIN TIPENVILVL SGLFRSLQSN EKILLLCLAE NLDISEVKNG ILSDFAFDKN IFQLHKPSKE NITRYFSNLI ELLKTKPSDI PMKKRRVKPL PELQKVTSNA APTNFDENGE PLSEKVVLRR KLKSFQHQDM RLKNVLKIKL SGLMDLFKNR YKRFRKPPID DAFLVHLFEP ETSNDPNWQP AYIKDENMIL EVSTGRKFFN MDLDIVEERL WNGYYSEPKQ FLKDIELIYR DANTIGDRER VIKASEMFAN AQMGIEEIST PDFIQECKAT RQRDLERQEL FLEDEEKRAA MELEAKEQSQ ENILQEPDLK DNKANEFGVA AGNQLQAQLQ TTINTASIVN NSEVPQPIDT NLYKKEIPAA IPSAVDKEKA VIPEDSGANE EYTTELIQAT CTSEITTDDD ERARKEPKEN EDSLQTQVTE ENFSKIDANT NNINHVKEIQ SVNKPNSLHE TVEKRERSPI PKEVVEPEQG KKSDKELILT PEQIKKVSAC LIEHCQNFTV SQLEDVHSSV AKIIWKSKSA WDKTGTVDEI IKFLSE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
150.0 mMKClpotassium chloride
25.0 mMHEPES-Potassium hydroxide
1.0 mMEthylenediaminetetraacetic acid
4.0 mMMgCl2Magnesium chloride
2.0 mM2-mercaptoethanol
2.0 mMATPrS
0.025 v/voctyl D-glucoside

Details: Solution was made fresh and detergent was added to solve preference orientation issue.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GOLD / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Blot 3S, blot forth 3.
DetailsThe sample was a novel chromatin remodeler and a AAA+ ATPase.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 193.0 K / Max: 193.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Details: A total of 75 frames were recorded for each micrograph stack.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jq0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109554
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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