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- EMDB-20235: Structure of a complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20235
TitleStructure of a complex
Map dataComposite map created by combining the best parts of consensus and multi-body maps
Sample
  • Complex: enzymatic complex with ligands
    • Protein or peptide: DNA polymerase delta catalytic subunit
    • Protein or peptide: DNA polymerase delta small subunit
    • Protein or peptide: DNA polymerase delta subunit 3
    • DNA: DNA (30-MER)
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: water
KeywordsDNA binding / enzyme / catalysis / regulation / DNA BINDING PROTEIN / dna binding protein-dna complex
Function / homology
Function and homology information


delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity ...delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA strand elongation involved in DNA replication / DNA metabolic process / leading strand elongation / mismatch repair / base-excision repair, gap-filling / replication fork / nucleotide-excision repair / base-excision repair / DNA-templated DNA replication / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / molecular adaptor activity / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain / DNA polymerase family B signature. ...DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase delta catalytic subunit / DNA polymerase delta small subunit / DNA polymerase delta subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJain R / Rice W / Aggarwal AK
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme.
Authors: Rinku Jain / William J Rice / Radhika Malik / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal /
Abstract: DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. ...DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.
History
DepositionMay 19, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6p1h
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20235.png

Downloads & links

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Map

FileDownload / File: emd_20235.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map created by combining the best parts of consensus and multi-body maps
Voxel sizeX=Y=Z: 0.8549 Å
Density
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-20.528583999999999 - 42.971040000000002
Average (Standard dev.)0.010617818 (±1.0534836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.568 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85490.85490.8549
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z273.568273.568273.568
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-20.52942.9710.011

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Supplemental data

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Sample components

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Entire : enzymatic complex with ligands

EntireName: enzymatic complex with ligands
Components
  • Complex: enzymatic complex with ligands
    • Protein or peptide: DNA polymerase delta catalytic subunit
    • Protein or peptide: DNA polymerase delta small subunit
    • Protein or peptide: DNA polymerase delta subunit 3
    • DNA: DNA (30-MER)
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: water

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Supramolecule #1: enzymatic complex with ligands

SupramoleculeName: enzymatic complex with ligands / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: DNA polymerase delta catalytic subunit

MacromoleculeName: DNA polymerase delta catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 127.438164 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDYKDDDDKG DHNHRHKHGD PHMSEKRSLP MVDVKIDDED TPQLEKKIKR QSIDHGVGSE PVSTIEIIPS DSFRKYNSQG FKAKDTDLM GTQLESTFEQ ELSQMEHDMA DQEEHDLSSF ERKKLPTDFD PSLYDISFQQ IDAEQSVLNG IKDENTSTVV R FFGVTSEG ...String:
MDYKDDDDKG DHNHRHKHGD PHMSEKRSLP MVDVKIDDED TPQLEKKIKR QSIDHGVGSE PVSTIEIIPS DSFRKYNSQG FKAKDTDLM GTQLESTFEQ ELSQMEHDMA DQEEHDLSSF ERKKLPTDFD PSLYDISFQQ IDAEQSVLNG IKDENTSTVV R FFGVTSEG HSVLCNVTGF KNYLYVPAPN SSDANDQEQI NKFVHYLNET FDHAIDSIEV VSKQSIWGYS GDTKLPFWKI YV TYPHMVN KLRTAFERGH LSFNSWFSNG TTTYDNIAYT LRLMVDCGIV GMSWITLPKG KYSMIEPNNR VSSCQLEVSI NYR NLIAHP AEGDWSHTAP LRIMSFDIEC AGRIGVFPEP EYDPVIQIAN VVSIAGAKKP FIRNVFTLNT CSPITGSMIF SHAT EEEML SNWRNFIIKV DPDVIIGYNT TNFDIPYLLN RAKALKVNDF PYFGRLKTVK QEIKESVFSS KAYGTRETKN VNIDG RLQL DLLQFIQREY KLRSYTLNAV SAHFLGEQKE DVHYSIISDL QNGDSETRRR LAVYCLKDAY LPLRLMEKLM ALVNYT EMA RVTGVPFSYL LARGQQIKVV SQLFRKCLEI DTVIPNMQSQ ASDDQYEGAT VIEPIRGYYD VPIATLDFNS LYPSIMM AH NLCYTTLCNK ATVERLNLKI DEDYVITPNG DYFVTTKRRR GILPIILDEL ISARKRAKKD LRDEKDPFKR DVLNGRQL A LKISANSVYG FTGATVGKLP CLAISSSVTA YGRTMILKTK TAVQEKYCIK NGYKHDAVVV YGDTDSVMVK FGTTDLKEA MDLGTEAAKY VSTLFKHPIN LEFEKAYFPY LLINKKRYAG LFWTNPDKFD KLDQKGLASV RRDSCSLVSI VMNKVLKKIL IERNVDGAL AFVRETINDI LHNRVDISKL IISKTLAPNY TNPQPHAVLA ERMKRREGVG PNVGDRVDYV IIGGNDKLYN R AEDPLFVL ENNIQVDSRY YLTNQLQNPI ISIVAPIIGD KQANGMFVVK SIKINTGSQK GGLMSFIKKV EACKSCKGPL RK GEGPLCS NCLARSGELY IKALYDVRDL EEKYSRLWTQ CQRCAGNLHS EVLCSNKNCD IFYMRVKVKK ELQEKVEQLS KW

UniProtKB: DNA polymerase delta catalytic subunit

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Macromolecule #2: DNA polymerase delta small subunit

MacromoleculeName: DNA polymerase delta small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.987352 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GPGGDLHMDA LLTKFNEDRS LQDENLSQPR TRVRIVDDNL YNKSNPFQLC YKKRDYGSQY YHIYQYRLKT FRERVLKECD KRWDAGFTL NGQLVLKKDK VLDIQGNQPC WCVGSIYCEM KYKPNVLDEV INDTYGAPDL TKSYTDKEGG SDEIMLEDES G RVLLVGDF ...String:
GPGGDLHMDA LLTKFNEDRS LQDENLSQPR TRVRIVDDNL YNKSNPFQLC YKKRDYGSQY YHIYQYRLKT FRERVLKECD KRWDAGFTL NGQLVLKKDK VLDIQGNQPC WCVGSIYCEM KYKPNVLDEV INDTYGAPDL TKSYTDKEGG SDEIMLEDES G RVLLVGDF IRSTPFITGV VVGILGMEAE AGTFQVLDIC YPTPLPQNPF PAPIATCPTR GKIALVSGLN LNNTSPDRLL RL EILREFL MGRINNKIDD ISLIGRLLIC GNSVDFDIKS VNKDELMISL TEFSKFLHNI LPSISVDIMP GTNDPSDKSL PQQ PFHKSL FDKSLESYFN GSNKEILNLV TNPYEFSYNG VDVLAVSGKN INDICKYVIP SNDNGESENK VEEGESNDFK DDIE HRLDL MECTMKWQNI APTAPDTLWC YPYTDKDPFV LDKWPHVYIV ANQPYFGTRV VEIGGKNIKI ISVPEFSSTG MIILL DLET LEAETVKIDI

UniProtKB: DNA polymerase delta small subunit

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Macromolecule #3: DNA polymerase delta subunit 3

MacromoleculeName: DNA polymerase delta subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 40.377715 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDQKASYFIN EKLFTEVKPV LFTDLIHHLK IGPSMAKKLM FDYYKQTTNA KYNCVVICCY KDQTIKIIHD LSNIPQQDSI IDCFIYAFN PMDSFIPYYD IIDQKDCLTI KNSYELKVSE SSKIIERTKT LEEKSKPLVR PTARSKTTPE ETTGRKSKSK D MGLRSTAL ...String:
MDQKASYFIN EKLFTEVKPV LFTDLIHHLK IGPSMAKKLM FDYYKQTTNA KYNCVVICCY KDQTIKIIHD LSNIPQQDSI IDCFIYAFN PMDSFIPYYD IIDQKDCLTI KNSYELKVSE SSKIIERTKT LEEKSKPLVR PTARSKTTPE ETTGRKSKSK D MGLRSTAL LAKMKKDRDD KETSRQNELR KRKEENLQKI NKQNPEREAQ MKELNNLFVE DDLDTEEVNG GSKPNSPKET DS NDKDKNN DDLEDLLETT AEDSLMDVPK IQQTKPSETE HSKEPKSEEE PSSFIDEDGY IVTKRPATST PPRKPSPVVK RAL SSSKKQ ETPSSNKRLK KQGTLESFFK RKAK

UniProtKB: DNA polymerase delta subunit 3

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Macromolecule #4: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.247966 KDa
SequenceString:
(DT)(DA)(DA)(DT)(DG)(DG)(DT)(DA)(DG)(DG) (DG)(DG)(DA)(DG)(DG)(DA)(DA)(DA)(DT)(DT) (DC)(DC)(DT)(DC)(DC)(DC)(DC)(DT)(DA) (DC)

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #6: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DCP
Molecular weightTheoretical: 467.157 Da
Chemical component information

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 44 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration1.2 mg/mL
BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 166444

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6p1h:
Cryo-EM Structure of DNA Polymerase Delta Holoenzyme

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