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- EMDB-9870: CryoEM structure of Abo1 hexamer - ADP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9870
TitleCryoEM structure of Abo1 hexamer - ADP complex
Map data
Sample
  • Complex: Abo1
    • Protein or peptide: Uncharacterized AAA domain-containing protein C31G5.19
KeywordsAAA+ ATPase Histone chaperone / CHAPERONE
Function / homology
Function and homology information


ATP-dependent H3-H4 histone complex chaperone activity / nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / chromatin / ATP hydrolysis activity / ATP binding / nucleus
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-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 abo1
Similarity search - Component
Biological speciesSaccharomyces (fungus) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.44 Å
AuthorsCho C / Jang J
Funding support Korea, Republic Of, 5 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2016R1A2B3006293 Korea, Republic Of
National Research Foundation (NRF, Korea)2016K1A1A2912057 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A6A7052113 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2015H1D3A1066116 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2018R1D1A1B07047345 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone.
Authors: Carol Cho / Juwon Jang / Yujin Kang / Hiroki Watanabe / Takayuki Uchihashi / Seung Joong Kim / Koichi Kato / Ja Yil Lee / Ji-Joon Song /
Abstract: The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate ...The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate nucleosome density and chromatin dynamics. Here, we demonstrate that the fission yeast ATAD2 homolog, Abo1, deposits histone H3-H4 onto DNA in an ATP-hydrolysis-dependent manner by in vitro reconstitution and single-tethered DNA curtain assays. We present cryo-EM structures of an ATAD2 family ATPase to atomic resolution in three different nucleotide states, revealing unique structural features required for histone loading on DNA, and directly visualize the transitions of Abo1 from an asymmetric spiral (ATP-state) to a symmetric ring (ADP- and apo-states) using high-speed atomic force microscopy (HS-AFM). Furthermore, we find that the acidic pore of ATP-Abo1 binds a peptide substrate which is suggestive of a histone tail. Based on these results, we propose a model whereby Abo1 facilitates H3-H4 loading by utilizing ATP.
History
DepositionMar 27, 2019-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jpq
  • Surface level: 1.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jpq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9870.png

Downloads & links

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Map

FileDownload / File: emd_9870.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 250 pix.
= 335. Å		1.34 Å/pix.
x 250 pix.
= 335. Å		1.34 Å/pix.
x 250 pix.
= 335. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4 / Movie #1: 1.4
Minimum - Maximum-5.1223264 - 10.447232
Average (Standard dev.)-0.034447398 (±0.57552564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 335.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z335.000335.000335.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-5.12210.447-0.034

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Supplemental data

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Sample components

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Entire : Abo1

EntireName: Abo1
Components
  • Complex: Abo1
    • Protein or peptide: Uncharacterized AAA domain-containing protein C31G5.19

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Supramolecule #1: Abo1

SupramoleculeName: Abo1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces (fungus)

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Macromolecule #1: Uncharacterized AAA domain-containing protein C31G5.19

MacromoleculeName: Uncharacterized AAA domain-containing protein C31G5.19
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 136.227438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAMGSGIQMK EEASEHGGSA DETQELSPVS DSSDEMPNNA KRRRRSQSMI ANKRIHQAFQ EDEGDEDWEE EEHKPKAKRR YNTRSNESF SEGDDEPFEV SESSALEDEL SDSEDSFIRS VRSKPKYKPG TRRSTRLRNR RSQDEEESEE EHRPILRERT S RINYSVPL ...String:
GAMGSGIQMK EEASEHGGSA DETQELSPVS DSSDEMPNNA KRRRRSQSMI ANKRIHQAFQ EDEGDEDWEE EEHKPKAKRR YNTRSNESF SEGDDEPFEV SESSALEDEL SDSEDSFIRS VRSKPKYKPG TRRSTRLRNR RSQDEEESEE EHRPILRERT S RINYSVPL AFPPVDEMDG DPSSQVNQSR SRKTHSELAI TKLLRQQVSS FMPYIDSSGS ESESDNTRIK KSSAKTIKAL TD PANSGGP PDFGRIREKS DLADSDPLGV DSSLSFESVG GLDNYINQLK EMVMLPLLYP EIFQRFNMQP PRGVLFHGPP GTG KTLMAR ALAAACSSEN KKVSFYMRKG ADCLSKWVGE AERQLRLLFE EAKSTQPSII FFDEIDGLAP VRSSKQEQIH ASIV STLLA LMDGMESRGQ VIIIGATNRP DAVDPALRRP GRFDREFYFP LPDRDARKKI IEIHTRNWDP PVPEWLCSML AEKSK GYGG ADLRALCTEA ALNSIKRTYP QLYRSTKRLQ IDPKTIKVKV KDFVMSMKRM IPSSERSSIS PSKPLSPELK PLLNEA FQD IEKTLQKLMP VASKLNPLEE VMYDDPKEND FEYQQRLETF ETLRIYKPRF LICGRKGLGQ TALGPAILQQ YEGVHVQ SF DMSTLLQDST QSIETSIIHL FLEVRRHTPS IIYIPDIDNW LNVLPLTAIT TFSSMLERLD FSDQILFLAL SSSPLSEL H PQLREWFSSK QSVYSLQYPT RDSIIAFFQP ILELIKASPT ELPGGIPRKR RVLPELPLAP DPPPFTSQKI TLKQTKQAD MRLLNKLKIK LNALLGSLRA RYRKFKKPLI DFNDIYCVDP ETGHSYRSRE ECHYEFVDDV VKQIGSDQKF SMMSLEEIEK RTWDNCYCT PKQFVHDIKL ILRDALQLED SETIKRAQEM YANVLLGVED MEDDQFSQRC ERMALREAER RKLRHGKLQK H LDETKADM QFTSEKPSVD ESITEVDDAI KDGPPVLAET LTNSLMEDVG PENVDMDIED NEIFTNQSTM SVPSMLVENE ES PKPDEYI DQKDKVQSPL LNGKSPVGVP SEAALRVSTD VSTNISSNGR ADIPVDTLIT SPADVPNNAP TDAHNITSAD GHI ENIEQE VVFPDLVFDE DRLTPLKQLL IDSTTGFTVD QLLHLHSFLY QIIWNTKSEW NRNSVVDECE RAVKEFMINA LQ

UniProtKB: ATPase histone chaperone abo1

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53582
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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