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- EMDB-9872: CryoEM structure of Abo1 Walker B (E372Q) mutant hexamer - ATP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9872
TitleCryoEM structure of Abo1 Walker B (E372Q) mutant hexamer - ATP complex
Map data
Sample
  • Complex: Abo1
    • Protein or peptide: unknown substrate
  • Protein or peptide: Uncharacterized AAA domain-containing protein C31G5.19
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


ATP-dependent H3-H4 histone complex chaperone activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / chromatin / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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 972h- (yeast) / Spodoptera frugiperda (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsCho C / Jang J / Song JJ
Funding support Korea, Republic Of, 5 items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1A2B3006293 Korea, Republic Of
National Research Foundation (Korea)2018R1A6A7052113 Korea, Republic Of
National Research Foundation (Korea)2016K1A1A2912057 Korea, Republic Of
National Research Foundation (Korea)NRF-2018R1D1A1B07047345 Korea, Republic Of
National Research Foundation (Korea)NRF-2015H1D3A1066116 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 28, 2019-
Header (metadata) releaseDec 25, 2019-
Map releaseDec 25, 2019-
UpdateJan 1, 2020-
Current statusJan 1, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jq0
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9872.png

Downloads & links

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Map

FileDownload / File: emd_9872.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-21.482294 - 33.6985
Average (Standard dev.)-0.0300527 (±1.2329776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 380.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z380.800380.800380.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281048
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-21.48233.699-0.030

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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: unknown substrate
  • Protein or peptide: Uncharacterized AAA domain-containing protein C31G5.19
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Abo1

SupramoleculeName: Abo1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Saccharomyces (fungus)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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 972h- (yeast)
Molecular weightTheoretical: 136.226453 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 FFDQIDGLAP 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

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Macromolecule #2: unknown substrate

MacromoleculeName: unknown substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 1.209482 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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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

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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: 1.0 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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99421
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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