+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28597 | |||||||||
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Title | Class1 of the INO80-Hexasome complex | |||||||||
Map data | INO80-Hex Complex, Class1, Overall | |||||||||
Sample |
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Keywords | Chromatin Remodeler / hexasome / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information R2TP complex / Swr1 complex / regulation of TOR signaling / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / 5'-3' DNA helicase activity / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity ...R2TP complex / Swr1 complex / regulation of TOR signaling / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / 5'-3' DNA helicase activity / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA duplex unwinding / subtelomeric heterochromatin formation / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / histone binding / DNA helicase / transcription by RNA polymerase II / chromosome, telomeric region / protein stabilization / chromatin remodeling / DNA repair / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
Authors | Wu H / Munoz E / Gourdet M / Cheng YF / Narlikar G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2023 Title: Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Authors: Hao Wu / Elise N Muñoz / Laura J Hsieh / Un Seng Chio / Muryam A Gourdet / Geeta J Narlikar / Yifan Cheng / Abstract: Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report ...Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location -2 (SHL -2), in contrast to SHL -6 and SHL -7, as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes such that Ino80 is maximally active near SHL -2. The SHL -2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that subnucleosomal particles play considerable regulatory roles. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28597.map.gz | 223.3 MB | EMDB map data format | |
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Header (meta data) | emd-28597-v30.xml emd-28597.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
Images | emd_28597.png | 122.9 KB | ||
Others | emd_28597_additional_1.map.gz emd_28597_half_map_1.map.gz emd_28597_half_map_2.map.gz | 8.2 MB 263.7 MB 263.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28597 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28597 | HTTPS FTP |
-Related structure data
Related structure data | 8etsMC 8ettC 8etuC 8etvC 8etwC 8eu2C 8eu9C 8eueC 8eufC 8eujC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28597.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | INO80-Hex Complex, Class1, Overall | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: INO80-Hex Complex, Class1, Hexasome
File | emd_28597_additional_1.map | ||||||||||||
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Annotation | INO80-Hex Complex, Class1, Hexasome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: INO80-Hex Complex, Class1, Overall, halfmap2
File | emd_28597_half_map_1.map | ||||||||||||
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Annotation | INO80-Hex Complex, Class1, Overall, halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: INO80-Hex Complex, Class1, Overall, halfmap1
File | emd_28597_half_map_2.map | ||||||||||||
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Annotation | INO80-Hex Complex, Class1, Overall, halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : INO80-Hex
Entire | Name: INO80-Hex |
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Components |
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-Supramolecule #1: INO80-Hex
Supramolecule | Name: INO80-Hex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Chromatin-remodeling ATPase INO80
Macromolecule | Name: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 54.985918 KDa |
Sequence | String: IEIDVLCDLT QRQAKLYQVL KSQISTNYDA IENAATNDST SNSASNSGSD QNLINAVMQF RKVCNHPDLF ERADVDSPFS FTTFGKTTS MLTASVANNN SSVISNSNMN LSSMSSNNIS NGKFTDLIYS SRNPIKYSLP RLIYEDLILP NYNNDVDIAN K LKNVKFNI ...String: IEIDVLCDLT QRQAKLYQVL KSQISTNYDA IENAATNDST SNSASNSGSD QNLINAVMQF RKVCNHPDLF ERADVDSPFS FTTFGKTTS MLTASVANNN SSVISNSNMN LSSMSSNNIS NGKFTDLIYS SRNPIKYSLP RLIYEDLILP NYNNDVDIAN K LKNVKFNI FNPSTNYELC LFLSKLTGEP SLNEFFRVST TPLLKRVIER TNGPKNTDSL SFKTITQELL EVTRNAPSEG VM ASLLNVE KHAYEREYLN CIQRGYHPNV SAPPVTIEVL GSSHVTNSIN NELFDPLISQ ALSDIPAITQ YNMHVKKGIP VED FPKTGL FPEPLNKNFS SNISMPSMDR FITESAKLRK LDELLVKLKS EGHRVLIYFQ MTKMMDLMEE YLTYRQYNHI RLDG SSKLE DRRDLVHDWQ TNPEIFVFLL STRAGGLGIN LTAADTVIFY DSDWNPTIDS QAMDRAHRLG QTRQVTVYRL LVRGT IEER M UniProtKB: Chromatin-remodeling ATPase INO80 |
-Macromolecule #2: Actin-related protein 5
Macromolecule | Name: Actin-related protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 86.522047 KDa |
Sequence | String: KAVVIDDPPL RQTPEPFDEQ SAYNPQSPIA IDFGSSKLRA GFVNHATPTH IFPNALTKFR DRKLNKNFTF VGNDTLLDQA VRSQSRSPF DGPFVTNWNL TEEILDYTFH HLGVVPDNGI PNPILLTERL ATVQSQRTNW YQILFETYNV PGVTFGIDSL F SFYNYNPS ...String: KAVVIDDPPL RQTPEPFDEQ SAYNPQSPIA IDFGSSKLRA GFVNHATPTH IFPNALTKFR DRKLNKNFTF VGNDTLLDQA VRSQSRSPF DGPFVTNWNL TEEILDYTFH HLGVVPDNGI PNPILLTERL ATVQSQRTNW YQILFETYNV PGVTFGIDSL F SFYNYNPS GNKTGLVISC GHEDTNVIPV VDGAGILTDA KRINWGGHQA VDYLNDLMAL KYPYFPTKMS YLQYETMYKD YC YVSRNYD EDIEKILTLE NLDTNDVVVE APFTEVLQPQ KTEEELRIQA EKRKETGKRL QEQARLKRME KLVQKQEEFE YFS KVRDQL IDEPKKKVLS VLQNAGFDDE RDFKKYLHSL EQSLKKAQMV EAEDDSHLDE MNEDKTAQKF DLLDIADEDL NEDQ IKEKR KQRFLKASQD ARQKAKEEKE RVAKEEEEKK LKEQQWRETD LNGWIKDKRL KLNKLIKRRK EKLKLRDEMK DRKSQ VSQN RMKNLASLAE DNVKQGAKRN RHQATIDNDP NDTFGANDED WLIYTDITQN PEAFEEALEY EYKDIVELER LLLEHD PNF TEEDTLEAQY DWRNSILHLF LRGPRPHDSE NIHEQHQMHL NVERIRVPEV IFQPTMGGQD QAGICELSET ILLKKFG SQ PGKLSQTSID MVNNVLITGG NAKVPGLKER IVKEFTGFLP TGTNITVNMS SDPSLDAWKG MAALARNEEQ YRKTVISK K EYEEYGPEYI KEHKLGNTKY FED UniProtKB: Actin-related protein 5 |
-Macromolecule #3: Chromatin-remodeling complex subunit IES6
Macromolecule | Name: Chromatin-remodeling complex subunit IES6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 15.881406 KDa |
Sequence | String: ERLLFLRSVG ERNEIGFPSR FKSAHYKKPT RRHKSARQLI SDENKRINAL LTKANKAAES STAARRLVPK ATYFSVEAPP SIRPAKKYC DVTGLKGFYK SPTNNIRYHN AEIYQLIVKP MAPGVDQEYL KLRGANFVLK UniProtKB: Chromatin-remodeling complex subunit IES6 |
-Macromolecule #4: RuvB-like protein 1
Macromolecule | Name: RuvB-like protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 48.543805 KDa |
Sequence | String: VTRTAAHTHI KGLGLDESGV AKRVEGGFVG QIEAREACGV IVDLIKAKKM SGRAILLAGG PSTGKTALAL AISQELGPKV PFCPLVGSE LYSVEVKKTE TLMENFRRAI GLRIKETKEV YEGEVTELTP EDAENPLGGY GKTISHVIVG LKSAKGTKTL R LDPTIYES ...String: VTRTAAHTHI KGLGLDESGV AKRVEGGFVG QIEAREACGV IVDLIKAKKM SGRAILLAGG PSTGKTALAL AISQELGPKV PFCPLVGSE LYSVEVKKTE TLMENFRRAI GLRIKETKEV YEGEVTELTP EDAENPLGGY GKTISHVIVG LKSAKGTKTL R LDPTIYES IQREKVSIGD VIYIEANTGA VKRVGRSDAY ATEFDLETEE YVPLPKGEVH KKKEIVQDVT LHDLDVANAR PQ GGQDVIS MMGQLLKPKK TEITEKLRQE VNKVVAKYID QGVAELIPGV LFIDEVNMLD IEIFTYLNKA LESNIAPVVV LAS NRGMTT VRGTEDVISP HGVPPDLIDR LLIVRTLPYD KDEIRTIIER RATVERLQVE SSALDLLATM GTETSLRYAL QLLA PCGIL AQTSNRKEIV VNDVNEAKLL FLDAKRSTKI LETSANYL UniProtKB: RuvB-like protein 1 |
-Macromolecule #5: RuvB-like protein 2
Macromolecule | Name: RuvB-like protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 50.153898 KDa |
Sequence | String: KSLSLIAAHS HITGLGLDEN LQPRPTSEGM VGQLQARRAA GVILKMVQNG TIAGRAVLVA GPPSTGKTAL AMGVSQSLGK DVPFTAIAG SEIFSLELSK TEALTQAFRK SIGIKIKEET ELIEGEVVEI QIDRSITGGH KQGKLTIKTT DMETIYELGN K MIDGLTKE ...String: KSLSLIAAHS HITGLGLDEN LQPRPTSEGM VGQLQARRAA GVILKMVQNG TIAGRAVLVA GPPSTGKTAL AMGVSQSLGK DVPFTAIAG SEIFSLELSK TEALTQAFRK SIGIKIKEET ELIEGEVVEI QIDRSITGGH KQGKLTIKTT DMETIYELGN K MIDGLTKE KVLAGDVISI DKASGKITKL GRSFARSRDY DAMGADTRFV QCPEGELQKR KTVVHTVSLH EIDVINSRTQ GF LALFTGD TGEIRSEVRD QINTKVAEWK EEGKAEIVPG VLFIDEVHML DIECFSFINR ALEDEFAPIV MMATNRGVSK TRG TNYKSP HGLPLDLLDR SIIITTKSYN EQEIKTILSI RAQEEEVELS SDALDLLTKT GVETSLRYSS NLISVAQQIA MKRK NNTVE VEDVKRAYLL FLDSARSVKY VQENESQYID DQGNVQISIA KSADPDAMDT TE UniProtKB: RuvB-like protein 2 |
-Macromolecule #6: Ino eighty subunit 2
Macromolecule | Name: Ino eighty subunit 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 3.531075 KDa |
Sequence | String: FVKPRRPYNS EGMTRILRRY EEDLFCTF UniProtKB: Ino eighty subunit 2 |
-Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: OTHER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 67.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76874 |