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Yorodumi- EMDB-0244: Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex... -
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-Basic information
Entry | Database: EMDB / ID: EMD-0244 | |||||||||
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Title | Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA | |||||||||
Map data | cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA | |||||||||
Sample |
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Keywords | DNA / polymerase D / Pyrococcus / REPLICATION | |||||||||
Function / homology | Function and homology information exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / DNA catabolic process / DNA strand elongation involved in DNA replication / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | |||||||||
Biological species | Pyrococcus abyssi (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Raia P / Carroni M | |||||||||
Funding support | France, 1 items
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Citation | Journal: PLoS Biol / Year: 2019 Title: Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. Authors: Pierre Raia / Marta Carroni / Etienne Henry / Gérard Pehau-Arnaudet / Sébastien Brûlé / Pierre Béguin / Ghislaine Henneke / Erik Lindahl / Marc Delarue / Ludovic Sauguet / Abstract: PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal ...PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome. | |||||||||
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_0244.map.gz | 38.3 MB | EMDB map data format | |
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Header (meta data) | emd-0244-v30.xml emd-0244.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
Images | emd_0244.png | 81.5 KB | ||
Filedesc metadata | emd-0244.cif.gz | 7 KB | ||
Others | emd_0244_half_map_1.map.gz emd_0244_half_map_2.map.gz | 37.7 MB 37.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0244 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0244 | HTTPS FTP |
-Validation report
Summary document | emd_0244_validation.pdf.gz | 531.5 KB | Display | EMDB validaton report |
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Full document | emd_0244_full_validation.pdf.gz | 530.7 KB | Display | |
Data in XML | emd_0244_validation.xml.gz | 10.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0244 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0244 | HTTPS FTP |
-Related structure data
Related structure data | 6hmsMC 6hmfC M: atomic model generated by this map C: citing same article (ref.) |
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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_0244.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: cryo-EM half map A of DNA polymerase D...
File | emd_0244_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map A of DNA polymerase D from Pyrococcus abyssi in complex with DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map B of DNA polymerase D...
File | emd_0244_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map B of DNA polymerase D from Pyrococcus abyssi in complex with DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex between DNA polymerase D and DNA duplex
Entire | Name: Complex between DNA polymerase D and DNA duplex |
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Components |
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-Supramolecule #1: Complex between DNA polymerase D and DNA duplex
Supramolecule | Name: Complex between DNA polymerase D and DNA duplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: DNA polymerase D
Supramolecule | Name: DNA polymerase D / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
-Macromolecule #1: DNA polymerase II small subunit
Macromolecule | Name: DNA polymerase II small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 45.078012 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: YEVKFVEAYA SLFKSRLSKL KRILRENPEI SNVVDIGKLN YVSGDEEVTI IGLVNSKRET NRGLIFEVED KTGIVKVFLP KDSEDYREA FKVLPDAVVA FKGFYSKKGI FFANKFYLPD VPLYRKQKPP LEEKVYAILI SDIHVGSREF CEKAFLKFLE W LNGHVESK ...String: YEVKFVEAYA SLFKSRLSKL KRILRENPEI SNVVDIGKLN YVSGDEEVTI IGLVNSKRET NRGLIFEVED KTGIVKVFLP KDSEDYREA FKVLPDAVVA FKGFYSKKGI FFANKFYLPD VPLYRKQKPP LEEKVYAILI SDIHVGSREF CEKAFLKFLE W LNGHVESK EEEEIVSRVK YLIIAGDVVD GIGIYPGQYS DLVIPDIFDQ YEALANLLAN VPEHITMFIG PGNADAARPA IP QPEFYKE YAKPIYKLKN AIIISNPAVI RLHGRDFLIA HGRGIEDVVS FVPGLTHHKP GLPMVELLKM RHLAPTFGGK VPI APDPED LLVIEEVPDL VQMGHVHVYD AVVYRGVQLV NSATWQAQTE FQKMVNIVPT PAKVPVVDVE SARVVKVLDF SGWC UniProtKB: DNA polymerase II small subunit |
-Macromolecule #2: DNA polymerase II large subunit,DNA polymerase II large subunit
Macromolecule | Name: DNA polymerase II large subunit,DNA polymerase II large subunit type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 144.418969 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MELPKEMEEY FEMLQREIDK AYEIAKKARA QGKDPSLDVE IPQATDMAGR VESLVGPPGV AKRIRELVKE YGKEIAALKI VDEIIEGKF GDLGSREKYA EQAVRTALAI LTEGIVSAPI EGIANVKIKR NTWADNSEYL ALYYAGPIRS SGGTAQALSV L VGDYVRRK ...String: MELPKEMEEY FEMLQREIDK AYEIAKKARA QGKDPSLDVE IPQATDMAGR VESLVGPPGV AKRIRELVKE YGKEIAALKI VDEIIEGKF GDLGSREKYA EQAVRTALAI LTEGIVSAPI EGIANVKIKR NTWADNSEYL ALYYAGPIRS SGGTAQALSV L VGDYVRRK LGLDRFKPSE KHIERMVEEV DLYHRAVTRL QYHPSPEEVR LAMRNIPIEI TGEATDDVEV SHRDVPGVET NQ LRGGAIL VLAEGVLQKA KKLVKYIDKM GIEGWEWLKE FVEAKEKGEP KEEGKEESLA ESTLEETKVE VDMGFYYSLY QKF KEEIAP SDKYAKEVIG GRPLFSDPSK PGGFRLRYGR SRASGFATWG INPATMILVD EFLAIGTQLK TERPGKGAVV TPVT TIEGP IVKLKDGSVL RVDDYNLALK VREDVEEILY LGDAVIAFGD FVENNQTLLP ANYCEEWWIL EFVKALKEIY EVHLE PFTE NEEESIEEAS DYLEIDPEFL KEMLRDPLRV KPPVELAIHF SEVLGIPLHP YYTLYWNSVE PKDVEKLWRL LKNYAE IEW SNFRGIKFAK KIVISQEKLG DSKRTLELLG LPHTVRDGNV IVDYPWAAAL LTPLGNLNWE FMAKPLYATI DIINENN EI KLRDRGISWI GARMGRPEKA KERKMKPPVQ VLFPIGLAGG SSRDIKKAAE EGKVAEVEIA FFKCPKCGHV GPEHLCPN C GTRKELLWVC PRCNAEYPES QAEGYNYTCP KCNVKLRPYA KRKIRPSELL NRAMENVKVY GVDKLKGVMG MTSGWKMPE PLEKGLLRAK NDVYVFKDGT IRFDATDAPI THFRPREIGV SVEKLRELGY THDFEGKPLV SEDQIVELKP QDIILSKEAG RYLLKVAKF VDDLLEKFYG LPRFYNAEKM EDLIGHLVIG LAPHTSAGIV GRIIGFVDAL VGYAHPYFHA AKRRNCDGDE D AVMLLLDA LLNFSRYYLP EKRGGKMDAP LVITTRLDPR EVDSEVHNMD IVRYYPLEFY EATYELKSPK ELVGVIERVE DR LGKPEMY YGLKFTHDTD DIALGPKMSL YKQLGDMEEK VRRQLEVAKR IRAVDEHGVA EKILNSHLIP DLRGNLRSFT RQE FRCVKC NTKFRRPPLN GKCPVCGGKI VLTVSKGAIE KYLGTAKMLV TEYNVKNYTR QRICLTERDI DSLFENVFPE TQLT LIVNP NDICQRLVMA RTGEVNKSGL LENLSNGSKK TEKAEKAEKP RKKSDEKPKK KRVISLEEFF SRKSK UniProtKB: DNA polymerase II large subunit, DNA polymerase II large subunit |
-Macromolecule #3: DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3')
Macromolecule | Name: DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 4.635998 KDa |
Sequence | String: (DG)(DA)(DG)(DA)(DC)(DG)(DG)(DG)(DC)(DC) (DG)(DC)(DG)(DT)(DC) |
-Macromolecule #4: DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3')
Macromolecule | Name: DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3') type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 4.851129 KDa |
Sequence | String: (DT)(DG)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC) (DC)(DG)(DT)(DC)(DT)(DC) |
-Macromolecule #5: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (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
Startup model | Type of model: OTHER / Details: SGD ab initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8774 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |