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- EMDB-28815: Cryo-EM of the S. cerevisiae chromatin remodeler Yta7 hexamer bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-28815
TitleCryo-EM of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to nucleosome
Map dataEM map un sharpen and vop gaussian processed
Sample
  • Complex: Yta7 and nucleosome complex
    • Protein or peptide: Yta7
KeywordsAAA+ ATPase / chromatin remodeler / TRANSFERASE
Function / homology
Function and homology information


ATP-dependent histone chaperone activity / positive regulation of invasive growth in response to glucose limitation / CENP-A containing chromatin assembly / nucleosome disassembly / ATP-dependent chromatin remodeler activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / chromosome, centromeric region / transcription initiation-coupled chromatin remodeling / DNA-templated DNA replication / nucleosome assembly ...ATP-dependent histone chaperone activity / positive regulation of invasive growth in response to glucose limitation / CENP-A containing chromatin assembly / nucleosome disassembly / ATP-dependent chromatin remodeler activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / chromosome, centromeric region / transcription initiation-coupled chromatin remodeling / DNA-templated DNA replication / nucleosome assembly / chromatin organization / chromosome / histone binding / chromatin remodeling / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / 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) / ATPase, AAA-type, core / Bromodomain profile. / Bromodomain / Bromodomain-like superfamily ...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) / ATPase, AAA-type, core / 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
ATPase histone chaperone YTA7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 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
DepositionNov 7, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28815.png

Downloads & links

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Map

FileDownload / File: emd_28815.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map un sharpen and vop gaussian processed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.31 Å/pix.
x 160 pix.
= 529.92 Å		3.31 Å/pix.
x 160 pix.
= 529.92 Å		3.31 Å/pix.
x 160 pix.
= 529.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.312 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.67
Minimum - Maximum-0.9849943 - 3.2470038
Average (Standard dev.)-0.009276352 (±0.16308689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 529.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map

Fileemd_28815_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_28815_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yta7 and nucleosome complex

EntireName: Yta7 and nucleosome complex
Components
  • Complex: Yta7 and nucleosome complex
    • Protein or peptide: Yta7

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Supramolecule #1: Yta7 and nucleosome complex

SupramoleculeName: Yta7 and nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Gra-fix fractions that contain Yta7 and nucleosome
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: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MARNLRNRRG SDVEDASNAK VGYETQIKDE NGIIHTTTRS LRKINYAEIE KVFDFLEDDQ VMDKDETPVD VTSDEHHNNN QKGDDEDDDV DLVSPHENAR TNEELTNERN LRKRKAHDPE EDDESFHEED VDDDEEEEEA DEFEDEYLDE DSKDNNRRRR AADRKFVVPD ...String:
MARNLRNRRG SDVEDASNAK VGYETQIKDE NGIIHTTTRS LRKINYAEIE KVFDFLEDDQ VMDKDETPVD VTSDEHHNNN QKGDDEDDDV DLVSPHENAR TNEELTNERN LRKRKAHDPE EDDESFHEED VDDDEEEEEA DEFEDEYLDE DSKDNNRRRR AADRKFVVPD PDDDEEYDED DEEGDRISHS ASSKRLKRAN SRRTRSSRHP ETPPPVRRAL RSRTRHSRTS NEENDDENDN SRNEALTLAD EIRELQEDSP IREKRFLRER TKPVNYKLPP PLTASNAEEF IDKNNNALSF HNPSPARRGR GGWNASQNSG PTRRLFPTGG PFGGNDVTTI FGKNTNFYNQ VPSAFSDNNN NKLILDSDSS DDEILPLGVT PKTKKENTQK KKKKKPEIAD LDPLGVDMNV NFDDIGGLDN YIDQLKEMVA LPLLYPELYQ NFNITPPRGV LFHGPPGTGK TLMARALAAS CSSDERKITF FMRKGADILS KWVGEAERQL RLLFEEAKKH QPSIIFFDEI DGLAPVRSSK QEQIHASIVS TLLALMDGMD NRGQVIVIGA TNRPDAVDPA LRRPGRFDRE FYFPLPDVKA RFKILQIQTR KWSSPLSTNF IDKLAFLTKG YGGADLRSLC TEAALISIQR SFPQIYRSND KLLVDPSKIK VKVSDFMLAL KKIVPSSARS TGSSPQPLPE LIKPLLADQL NNLKNKLDYM LNIKDTTFQR NTSLLQNFID YEEYSGEEEE HDKYGGNEDT SSFRSYEFFE SMAESQICKP RLLINGPKGN GQQYVGAAIL NYLEEFNVQN LDLASLVSES SRTIEAAVVQ SFMEAKKRQP SVVFIPNLDI WINTIPENVI LVLSGLFRSL QSNEKILLLC LAENLDISEV KNGILSDFAF DKNIFQLHKP SKENITRYFS NLIELLKTKP SDIPMKKRRV KPLPELQKVT SNAAPTNFDE NGEPLSEKVV LRRKLKSFQH QDMRLKNVLK IKLSGLMDLF KNRYKRFRKP PIDDAFLVHL FEPETSNDPN WQPAYIKDEN MILEVSTGRK FFNMDLDIVE ERLWNGYYSE PKQFLKDIEL IYRDANTIGD RERVIKASEM FANAQMGIEE ISTPDFIQEC KATRQRDLER QELFLEDEEK RAAMELEAKE QSQENILQEP DLKDNKANEF GVAAGNQLQA QLQTTINTAS IVNNSEVPQP IDTNLYKKEI PAAIPSAVDK EKAVIPEDSG ANEEYTTELI QATCTSEITT DDDERARKEP KENEDSLQTQ VTEENFSKID ANTNNINHVK EIQSVNKPNS LHETVEKRER SPIPKEVVEP EQGKKSDKEL ILTPEQIKKV SACLIEHCQN FTVSQLEDVH SSVAKIIWKS KSAWDKTGTV DEIIKFLSE

UniProtKB: ATPase histone chaperone YTA7

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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

Concentration3 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 mMATPgS
0.025 v/voctyl D-glucoside

Details: Solution was made fresh and detergent was added to solve a preference orientation issue.
GridModel: Quantifoil R2/1 / Support film - Material: GOLD / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Blot 3 seconds, blot force 3.
DetailsThe sample was a novel chromatin remodeler and an 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 was 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: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229854
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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