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- 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
TitleCryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Map datacryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Sample
  • Complex: Complex between DNA polymerase D and DNA duplex
    • Complex: DNA polymerase D
      • Protein or peptide: DNA polymerase II small subunit
      • Protein or peptide: DNA polymerase II large subunit,DNA polymerase II large subunit
    • Complex: DNA
      • DNA: DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3')
      • DNA: DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3')
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
KeywordsDNA / 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
DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2 / DNA polymerase II small subunit, archaeal / DNA polymerase delta/II small subunit family / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. ...DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2 / DNA polymerase II small subunit, archaeal / DNA polymerase delta/II small subunit family / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA polymerase II small subunit / DNA polymerase II large subunit
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsRaia P / Carroni M
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR -17-CE11-0005 France
CitationJournal: 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
DepositionSep 12, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseJan 30, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.58
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.58
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hms
  • Surface level: 0.58
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0244.png

Downloads & links

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Map

FileDownload / File: emd_0244.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.58 / Movie #1: 0.58
Minimum - Maximum-0.6584329 - 1.6239548
Average (Standard dev.)0.004671554 (±0.07651347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z299.200299.200299.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.6581.6240.005

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Supplemental data

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Half map: cryo-EM half map A of DNA polymerase D...

Fileemd_0244_half_map_1.map
Annotationcryo-EM half map A of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map B of DNA polymerase D...

Fileemd_0244_half_map_2.map
Annotationcryo-EM half map B of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between DNA polymerase D and DNA duplex

EntireName: Complex between DNA polymerase D and DNA duplex
Components
  • Complex: Complex between DNA polymerase D and DNA duplex
    • Complex: DNA polymerase D
      • Protein or peptide: DNA polymerase II small subunit
      • Protein or peptide: DNA polymerase II large subunit,DNA polymerase II large subunit
    • Complex: DNA
      • DNA: DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3')
      • DNA: DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3')
  • Ligand: FE (III) ION
  • Ligand: ZINC ION

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Supramolecule #1: Complex between DNA polymerase D and DNA duplex

SupramoleculeName: 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

SupramoleculeName: DNA polymerase D / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Pyrococcus abyssi (archaea)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Pyrococcus abyssi (archaea)

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Macromolecule #1: DNA polymerase II small subunit

MacromoleculeName: DNA polymerase II small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 45.078012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: DNA polymerase II large subunit,DNA polymerase II large subunit

MacromoleculeName: 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
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 144.418969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3')

MacromoleculeName: 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
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 4.635998 KDa
SequenceString:
(DG)(DA)(DG)(DA)(DC)(DG)(DG)(DG)(DC)(DC) (DG)(DC)(DG)(DT)(DC)

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Macromolecule #4: DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3')

MacromoleculeName: 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
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 4.851129 KDa
SequenceString:
(DT)(DG)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC) (DC)(DG)(DT)(DC)(DT)(DC)

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (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

Startup modelType of model: OTHER / Details: SGD ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8774
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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