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- EMDB-26696: Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 h... -

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Basic information

Entry
Database: EMDB / ID: EMD-26696
TitleCryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS and histone H3 tail in state II
Map dataPrimary map that sharpen by deep enhancer
Sample
  • Complex: Complex of Yta7 with H3N tail
    • Protein or peptide: ATPase histone chaperone YTA7
    • Protein or peptide: Histone H3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
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
ATPase histone chaperone YTA7 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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
DepositionApr 19, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26696.png

Downloads & links

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Map

FileDownload / File: emd_26696.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map that sharpen by deep enhancer
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0017853111 - 2.2284324
Average (Standard dev.)0.0016836062 (±0.030615246)
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_26696_additional_1.map
AnnotationRaw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Relion sharpen map

Fileemd_26696_additional_2.map
AnnotationRelion sharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26696_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26696_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 with H3N tail

EntireName: Complex of Yta7 with H3N tail
Components
  • Complex: Complex of Yta7 with H3N tail
    • Protein or peptide: ATPase histone chaperone YTA7
    • Protein or peptide: Histone H3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of Yta7 with H3N tail

SupramoleculeName: Complex of Yta7 with H3N tail / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Details: The translocation state of Histone 3 N-terminal peptide by Yta7
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 930 KDa

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Macromolecule #1: ATPase histone chaperone YTA7

MacromoleculeName: ATPase histone chaperone YTA7 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 162.182969 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString: HHHHHHHHHH TSGSMDYKDH DGDYKDHDID YKDDDDKMAR NLRNRRGSDV EDASNAKVGY ETQIKDENGI IHTTTRSLRK INYAEIEKV FDFLEDDQVM DKDETPVDVT SDEHHNNNQK GDDEDDDVDL VSPHENARTN EELTNERNLR KRKAHDPEED D ESFHEEDV ...String:
HHHHHHHHHH TSGSMDYKDH DGDYKDHDID YKDDDDKMAR NLRNRRGSDV EDASNAKVGY ETQIKDENGI IHTTTRSLRK INYAEIEKV FDFLEDDQVM DKDETPVDVT SDEHHNNNQK GDDEDDDVDL VSPHENARTN EELTNERNLR KRKAHDPEED D ESFHEEDV DDDEEEEEAD EFEDEYLDED SKDNNRRRRA ADRKFVVPDP DDDEEYDEDD EEGDRISHSA SSKRLKRANS RR TRSSRHP ETPPPVRRAL RSRTRHSRTS NEENDDENDN SRNEALTLAD EIRELQEDSP IREKRFLRER TKPVNYKLPP PLT ASNAEE FIDKNNNALS FHNPSPARRG RGGWNASQNS GPTRRLFPTG GPFGGNDVTT IFGKNTNFYN QVPSAFSDNN NNKL ILDSD SSDDEILPLG VTPKTKKENT QKKKKKKPEI ADLDPLGVDM NVNFDDIGGL DNYIDQLKEM VALPLLYPEL YQNFN ITPP RGVLFHGPPG TGKTLMARAL AASCSSDERK ITFFMRKGAD ILSKWVGEAE RQLRLLFEEA KKHQPSIIFF DEIDGL APV RSSKQEQIHA SIVSTLLALM DGMDNRGQVI VIGATNRPDA VDPALRRPGR FDREFYFPLP DVKARFKILQ IQTRKWS SP LSTNFIDKLA FLTKGYGGAD LRSLCTEAAL ISIQRSFPQI YRSNDKLLVD PSKIKVKVSD FMLALKKIVP SSARSTGS S PQPLPELIKP LLADQLNNLK NKLDYMLNIK DTTFQRNTSL LQNFIDYEEY SGEEEEHDKY GGNEDTSSFR SYEFFESMA ESQICKPRLL INGPKGNGQQ YVGAAILNYL EEFNVQNLDL ASLVSESSRT IEAAVVQSFM EAKKRQPSVV FIPNLDIWIN TIPENVILV LSGLFRSLQS NEKILLLCLA ENLDISEVKN GILSDFAFDK NIFQLHKPSK ENITRYFSNL IELLKTKPSD I PMKKRRVK PLPELQKVTS NAAPTNFDEN GEPLSEKVVL RRKLKSFQHQ DMRLKNVLKI KLSGLMDLFK NRYKRFRKPP ID DAFLVHL FEPETSNDPN WQPAYIKDEN MILEVSTGRK FFNMDLDIVE ERLWNGYYSE PKQFLKDIEL IYRDANTIGD RER VIKASE MFANAQMGIE EISTPDFIQE CKATRQRDLE RQELFLEDEE KRAAMELEAK EQSQENILQE PDLKDNKANE FGVA AGNQL QAQLQTTINT ASIVNNSEVP QPIDTNLYKK EIPAAIPSAV DKEKAVIPED SGANEEYTTE LIQATCTSEI TTDDD ERAR KEPKENEDSL QTQVTEENFS KIDANTNNIN HVKEIQSVNK PNSLHETVEK RERSPIPKEV VEPEQGKKSD KELILT PEQ IKKVSACLIE HCQNFTVSQL EDVHSSVAKI IWKSKSAWDK TGTVDEIIKF LSE

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Macromolecule #2: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.680181 KDa
SequenceString:
MARTKQTARK STGGKAPRKQ LASKA

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 5 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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-me2-mercaptoethanol
2.0 mMATPgS
0.025 v/vOctyl_glucosideoctyl 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 / Details: The grids were doulbe blots
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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.
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

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 431065
FSC plot (resolution estimation)

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Atomic model buiding 1

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

PDB-7uqj:
Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS and histone H3 tail in state II

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