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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20235 | |||||||||
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Title | Structure of a complex | |||||||||
![]() | Composite map created by combining the best parts of consensus and multi-body maps | |||||||||
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![]() | DNA binding / enzyme / catalysis / regulation / DNA BINDING PROTEIN / dna binding protein-dna complex | |||||||||
Function / homology | ![]() delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / lagging strand elongation / double-strand break repair via break-induced replication ...delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA metabolic process / DNA replication proofreading / DNA strand elongation involved in DNA replication / leading strand elongation / mismatch repair / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / nucleotide-excision repair / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / 4 iron, 4 sulfur cluster binding / DNA replication / molecular adaptor activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Jain R / Rice W / Aggarwal AK | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 92.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 159.2 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p1hMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Composite map created by combining the best parts of consensus and multi-body maps | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8549 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : enzymatic complex with ligands
Entire | Name: enzymatic complex with ligands |
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Components |
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-Supramolecule #1: enzymatic complex with ligands
Supramolecule | Name: enzymatic complex with ligands / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: DNA polymerase delta catalytic subunit
Macromolecule | Name: DNA polymerase delta catalytic 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: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 127.438164 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: DNA polymerase delta small subunit
Macromolecule | Name: DNA polymerase delta small 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: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 55.987352 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: DNA polymerase delta subunit 3
Macromolecule | Name: DNA polymerase delta subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 40.377715 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #4: DNA (30-MER)
Macromolecule | Name: DNA (30-MER) / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.247966 KDa |
Sequence | String: (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) |
-Macromolecule #5: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ![]() ChemComp-FS1: |
-Macromolecule #6: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Macromolecule | Name: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DCP |
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Molecular weight | Theoretical: 467.157 Da |
Chemical component information | ![]() ChemComp-DCP: |
-Macromolecule #7: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 44 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.2 mg/mL |
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Buffer | pH: 6.8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied 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 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-6p1h: |