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Yorodumi- EMDB-9872: CryoEM structure of Abo1 Walker B (E372Q) mutant hexamer - ATP complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9872 | ||||||||||||||||||
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Title | CryoEM structure of Abo1 Walker B (E372Q) mutant hexamer - ATP complex | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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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 | ||||||||||||||||||
Biological species | Saccharomyces (fungus) / Schizosaccharomyces pombe 972h- (yeast) / Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | ||||||||||||||||||
Authors | Cho C / Jang J / Song JJ | ||||||||||||||||||
Funding support | Korea, Republic Of, 5 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9872.map.gz | 139.2 MB | EMDB map data format | |
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Header (meta data) | emd-9872-v30.xml emd-9872.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_9872.png | 79.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9872 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9872 | HTTPS FTP |
-Validation report
Summary document | emd_9872_validation.pdf.gz | 540.2 KB | Display | EMDB validaton report |
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Full document | emd_9872_full_validation.pdf.gz | 539.7 KB | Display | |
Data in XML | emd_9872_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_9872_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9872 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9872 | HTTPS FTP |
-Related structure data
Related structure data | 6jq0MC 0800C 9870C 9871C 6jpqC 6jpuC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9872.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Abo1
Entire | Name: Abo1 |
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Components |
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-Supramolecule #1: Abo1
Supramolecule | Name: Abo1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 |
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Source (natural) | Organism: Saccharomyces (fungus) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Uncharacterized AAA domain-containing protein C31G5.19
Macromolecule | Name: Uncharacterized AAA domain-containing protein C31G5.19 type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) |
Molecular weight | Theoretical: 136.226453 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: unknown substrate
Macromolecule | Name: unknown substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 1.209482 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99421 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |