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- EMDB-22803: Cryo-EM 3D map of the Saccharomyces cerevisiae replicative polyme... -

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Basic information

Entry
Database: EMDB / ID: EMD-22803
TitleCryo-EM 3D map of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp
Map dataReplicative polymerase delta in complex with a primer/template and the PCNA clamp
Sample
  • Complex: Pol delta-PCNA-DNA
    • Complex: dsDNADNA
      • DNA: DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')
      • DNA: DNA (25-MER)
    • Complex: ProteinsProtein
      • Protein or peptide: Proliferating cell nuclear antigen
      • Protein or peptide: DNA polymerase
      • Protein or peptide: POL31 isoform 1
      • Protein or peptide: POL32 isoform 1
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
Function / homology
Function and homology information


delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / RNA-templated DNA biosynthetic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / DNA replication, removal of RNA primer ...delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / RNA-templated DNA biosynthetic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / DNA replication, removal of RNA primer / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / nucleotide-excision repair, DNA gap filling / maintenance of DNA trinucleotide repeats / PCNA complex / DNA replication proofreading / 3'-5'-DNA exonuclease activity / establishment of mitotic sister chromatid cohesion / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / silent mating-type cassette heterochromatin formation / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA strand elongation involved in DNA replication / mitotic sister chromatid cohesion / DNA metabolic process / leading strand elongation / DNA polymerase processivity factor activity / error-free translesion synthesis / regulation of DNA replication / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA replication / base-excision repair, gap-filling / positive regulation of DNA repair / replication fork / nucleotide-excision repair / base-excision repair / DNA-templated DNA replication / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / molecular adaptor activity / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / identical protein 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 / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / DNA polymerase delta/II small subunit family / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site ...DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / DNA polymerase delta/II small subunit family / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / 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
BJ4_G0010060.mRNA.1.CDS.1 / POL31 isoform 1 / DNA polymerase / Proliferating cell nuclear antigen / DNA polymerase delta catalytic subunit / Proliferating cell nuclear antigen / DNA polymerase delta small subunit / DNA polymerase delta subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZheng F / Georgescu R / Li H / O'Donnell ME
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115809 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of eukaryotic DNA polymerase δ bound to the PCNA clamp while encircling DNA.
Authors: Fengwei Zheng / Roxana E Georgescu / Huilin Li / Michael E O'Donnell /
Abstract: The DNA polymerase (Pol) δ of (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and ...The DNA polymerase (Pol) δ of (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and functions in genome replication, repair, and recombination. Unique among DNA polymerases, the Pol3 catalytic subunit contains a 4Fe-4S cluster that may sense the cellular redox state. Here we report the 3.2-Å cryo-EM structure of S.c. Pol δ in complex with primed DNA, an incoming ddTTP, and the PCNA clamp. Unexpectedly, Pol δ binds only one subunit of the PCNA trimer. This singular yet extensive interaction holds DNA such that the 2-nm-wide DNA threads through the center of the 3-nm interior channel of the clamp without directly contacting the protein. Thus, a water-mediated clamp and DNA interface enables the PCNA clamp to "waterskate" along the duplex with minimum drag. Pol31 and Pol32 are positioned off to the side of the catalytic Pol3-PCNA-DNA axis. We show here that Pol31-Pol32 binds single-stranded DNA that we propose underlies polymerase recycling during lagging strand synthesis, in analogy to replicase. Interestingly, the 4Fe-4S cluster in the C-terminal CysB domain of Pol3 forms the central interface to Pol31-Pol32, and this strategic location may explain the regulation of the oxidation state on Pol δ activity, possibly useful during cellular oxidative stress. Importantly, human cancer and other disease mutations map to nearly every domain of Pol3, suggesting that all aspects of Pol δ replication are important to human health and disease.
History
DepositionOct 4, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kc0
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22803.png

Downloads & links

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Map

FileDownload / File: emd_22803.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReplicative polymerase delta in complex with a primer/template and the PCNA clamp
Voxel sizeX=Y=Z: 0.826 Å
Density
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.44814953 - 1.967878
Average (Standard dev.)0.00042513688 (±0.032276735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 346.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8260.8260.826
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z346.920346.920346.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.4481.9680.000

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Supplemental data

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Sample components

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Entire : Pol delta-PCNA-DNA

EntireName: Pol delta-PCNA-DNA
Components
  • Complex: Pol delta-PCNA-DNA
    • Complex: dsDNADNA
      • DNA: DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')
      • DNA: DNA (25-MER)
    • Complex: ProteinsProtein
      • Protein or peptide: Proliferating cell nuclear antigen
      • Protein or peptide: DNA polymerase
      • Protein or peptide: POL31 isoform 1
      • Protein or peptide: POL32 isoform 1
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Pol delta-PCNA-DNA

SupramoleculeName: Pol delta-PCNA-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: dsDNA

SupramoleculeName: dsDNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Proteins

SupramoleculeName: Proteins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP...

MacromoleculeName: DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.681985 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DT)(DG)(DA)(DT)(DT)(DA)(DC)(DG)(DA) (DA)(DT)(DT)(DG)(DC)

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Macromolecule #2: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.677539 KDa
SequenceString:
(DC)(DT)(DG)(DC)(DA)(DC)(DG)(DA)(DA)(DT) (DT)(DA)(DA)(DG)(DC)(DA)(DA)(DT)(DT)(DC) (DG)(DT)(DA)(DA)(DT)(DC)(DA)(DT)(DG) (DG)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DT)

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Macromolecule #3: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.944051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLEAKFEEAS LFKRIIDGFK DCVQLVNFQC KEDGIIAQAV DDSRVLLVSL EIGVEAFQEY RCDHPVTLGM DLTSLSKILR CGNNTDTLT LIADNTPDSI ILLFEDTKKD RIAEYSLKLM DIDADFLKIE ELQYDSTLSL PSSEFSKIVR DLSQLSDSIN I MITKETIK ...String:
MLEAKFEEAS LFKRIIDGFK DCVQLVNFQC KEDGIIAQAV DDSRVLLVSL EIGVEAFQEY RCDHPVTLGM DLTSLSKILR CGNNTDTLT LIADNTPDSI ILLFEDTKKD RIAEYSLKLM DIDADFLKIE ELQYDSTLSL PSSEFSKIVR DLSQLSDSIN I MITKETIK FVADGDIGSG SVIIKPFVDM EHPETSIKLE MDQPVDLTFG AKYLLDIIKG SSLSDRVGIR LSSEAPALFQ FD LKSGFLQ FFLAPKFNDE E

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Macromolecule #4: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 124.707359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEKRSLPMV DVKIDDEDTP QLEKKIKRQS IDHGVGSEPV STIEIIPSDS FRKYNSQGFK AKDTDLMGTQ LESTFEQELS QMEHDMADQ EEHDLSSFER KKLPTDFDPS LYDISFQQID AEQSVLNGIK DENTSTVVRF FGVTSEGHSV LCNVTGFKNY L YVPAPNSS ...String:
MSEKRSLPMV DVKIDDEDTP QLEKKIKRQS IDHGVGSEPV STIEIIPSDS FRKYNSQGFK AKDTDLMGTQ LESTFEQELS QMEHDMADQ EEHDLSSFER KKLPTDFDPS LYDISFQQID AEQSVLNGIK DENTSTVVRF FGVTSEGHSV LCNVTGFKNY L YVPAPNSS DANDQEQINK FVHYLNETFD HAIDSIEVVS KQSIWGYSGD TKLPFWKIYV TYPHMVNKLR TAFERGHLSF NS WFSNGTT TYDNIAYTLR LMVDCGIVGM SWITLPKGKY SMIEPNNRVS SCQLEVSINY RNLIAHPAEG DWSHTAPLRI MSF SISCAG RIGVFPEPEY DPVIQIANVV SIAGAKKPFI RNVFTLNTCS PITGSMIFSH ATEEEMLSNW RNFIIKVDPD VIIG YNTTN FDIPYLLNRA KALKVNDFPY FGRLKTVKQE IKESVFSSKA YGTRETKNVN IDGRLQLDLL QFIQREYKLR SYTLN AVSA HFLGEQKEDV HYSIISDLQN GDSETRRRLA VYCLKDAYLP LRLMEKLMAL VNYTEMARVT GVPFSYLLAR GQQIKV VSQ LFRKCLEIDT VIPNMQSQAS DDQYEGATVI EPIRGYYDVP IATLDFNSLY PSIMMAHNLC YTTLCNKATV ERLNLKI DE DYVITPNGDY FVTTKRRRGI LPIILDELIS ARKRAKKDLR DEKDPFKRDV LNGRQLALKI SANSVYGFTG ATVGKLPC L AISSSVTAYG RTMILKTKTA VQEKYCIKNG YKHDAVVVYG DTDSVMVKFG TTDLKEAMDL GTEAAKYVST LFKHPINLE FEKAYFPYLL INKKRYAGLF WTNPDKFDKL DQKGLASVRR DSCSLVSIVM NKVLKKILIE RNVDGALAFV RETINDILHN RVDISKLII SKTLAPNYTN PQPHAVLAER MKRREGVGPN VGDRVDYVII GGNDKLYNRA EDPLFVLENN IQVDSRYYLT N QLQNPIIS IVAPIIGDKQ ANGMFVVKSI KINTGSQKGG LMSFIKKVEA CKSCKGPLRK GEGPLCSNCL ARSGELYIKA LY DVRDLEE KYSRLWTQCQ RCAGNLHSEV LCSNKNCDIF YMRVKVKKEL QEKVEQLSKW

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Macromolecule #5: POL31 isoform 1

MacromoleculeName: POL31 isoform 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 55.352688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDALLTKFNE DRSLQDENLS QPRTRVRIVD DNLYNKSNPF QLCYKKRDYG SQYYHIYQYR LKTFRERVLK ECDKRWDAGF TLNGQLVLK KDKVLDIQGN QPCWCVGSIY CEMKYKPNVL DEVINDTYGA PDLTKSYTDK EGGSDEIMLE DESGRVLLVG D FIRSTPFI ...String:
MDALLTKFNE DRSLQDENLS QPRTRVRIVD DNLYNKSNPF QLCYKKRDYG SQYYHIYQYR LKTFRERVLK ECDKRWDAGF TLNGQLVLK KDKVLDIQGN QPCWCVGSIY CEMKYKPNVL DEVINDTYGA PDLTKSYTDK EGGSDEIMLE DESGRVLLVG D FIRSTPFI TGVVVGILGM EAEAGTFQVL DICYPTPLPQ NPFPAPIATC PTRGKIALVS GLNLNNTSPD RLLRLEILRE FL MGRINNK IDDISLIGRL LICGNSVDFD IKSVNKDELM ISLTEFSKFL HNILPSISVD IMPGTNDPSD KSLPQQPFHK SLF DKSLES YFNGSNKEIL NLVTNPYEFS YNGVDVLAVS GKNINDICKY VIPSNDNGES ENKVEEGESN DFKDDIEHRL DLME CTMKW QNIAPTAPDT LWCYPYTDKD PFVLDKWPHV YIVANQPYFG TRVVEIGGKN IKIISVPEFS STGMIILLDL ETLEA ETVK IDI

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Macromolecule #6: POL32 isoform 1

MacromoleculeName: POL32 isoform 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 40.377715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 8 / 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 #9: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: D3T
Molecular weightTheoretical: 466.169 Da
Chemical component information

ChemComp-23T:
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 1 / 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: 7.5
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 K3 (6k x 4k) / Average electron dose: 68.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133468

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