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- EMDB-21115: Structure of DNA Polymerase Zeta/DNA/dNTP Ternary Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-21115
TitleStructure of DNA Polymerase Zeta/DNA/dNTP Ternary Complex
Map datacryosparc map
Sample
  • Complex: structure of DNA complex
    • Protein or peptide: DNA polymerase zeta catalytic subunit
    • Protein or peptide: DNA polymerase zeta processivity subunit
    • Protein or peptide: DNA polymerase delta small subunit
    • Protein or peptide: DNA polymerase delta subunit 3
    • DNA: DNA
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: CALCIUM ION
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsDNA REPLICATION / DNA REPAIR / TRANSLESION DNA SYNTHESIS / DNA POLYMERASE / DNA BINDING PROTEIN
Function / homology
Function and homology information


delta DNA polymerase complex / H3-H4 histone complex chaperone activity / 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 / Translesion synthesis by REV1 / Translesion synthesis by POLK ...delta DNA polymerase complex / H3-H4 histone complex chaperone activity / 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 / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / DNA metabolic process / DNA strand elongation involved in DNA replication / error-free translesion synthesis / leading strand elongation / mismatch repair / error-prone translesion synthesis / nucleotide-excision repair / double-strand break repair via homologous recombination / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin / mitochondrion / DNA binding / nucleus / metal ion binding / 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 zeta catalytic subunit / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain ...DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase zeta catalytic subunit / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional 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 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 zeta catalytic subunit / DNA polymerase zeta processivity subunit / DNA polymerase delta small subunit / DNA polymerase delta subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMalik R / Kopylov M / Jain R / Ubarrextena-Belandia I / Aggarwal AK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM124047 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structure and mechanism of B-family DNA polymerase ζ specialized for translesion DNA synthesis.
Authors: Radhika Malik / Mykhailo Kopylov / Yacob Gomez-Llorente / Rinku Jain / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal /
Abstract: DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its ...DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its importance in TLS, the structure of Polζ is unknown. We present cryo-EM structures of the Saccharomyces cerevisiae Polζ holoenzyme in the act of DNA synthesis (3.1 Å) and without DNA (4.1 Å). Polζ displays a pentameric ring-like architecture, with catalytic Rev3, accessory Pol31' Pol32 and two Rev7 subunits forming an uninterrupted daisy chain of protein-protein interactions. We also uncover the features that impose high fidelity during the nucleotide-incorporation step and those that accommodate mismatches and lesions during the extension reaction. Collectively, we decrypt the molecular underpinnings of Polζ's role in TLS and provide a framework for new cancer therapeutics.
History
DepositionDec 13, 2019-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v93
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21115.png

Downloads & links

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Map

FileDownload / File: emd_21115.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryosparc map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.752 Å		1.07 Å/pix.
x 256 pix.
= 274.752 Å		1.07 Å/pix.
x 256 pix.
= 274.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-17.639344999999999 - 44.019725999999999
Average (Standard dev.)0.0026207482 (±1.1028575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.752 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.073251.073251.07325
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z274.752274.752274.752
α/β/γ90.00090.00090.000
start NX/NY/NZ-205-205-205
NX/NY/NZ411411411
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-17.63944.0200.003

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Supplemental data

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Sample components

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Entire : structure of DNA complex

EntireName: structure of DNA complex
Components
  • Complex: structure of DNA complex
    • Protein or peptide: DNA polymerase zeta catalytic subunit
    • Protein or peptide: DNA polymerase zeta processivity subunit
    • Protein or peptide: DNA polymerase delta small subunit
    • Protein or peptide: DNA polymerase delta subunit 3
    • DNA: DNA
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: CALCIUM ION
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: water

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Supramolecule #1: structure of DNA complex

SupramoleculeName: structure of DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: DNA polymerase zeta catalytic subunit

MacromoleculeName: DNA polymerase zeta 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: 177.068516 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDYKDDDDKG DHNHRHKHGD PLEVLFQGPG GDPHMSRESN DTIQSDTVRS SSKSDYFRIQ LNNQDYYMSK PTFLDPSHGE SLPLNQFSQ VPNIRVFGAL PTGHQVLCHV HGILPYMFIK YDGQITDTST LRHQRCAQVH KTLEVKIRAS FKRKKDDKHD L AGDKLGNL ...String:
MDYKDDDDKG DHNHRHKHGD PLEVLFQGPG GDPHMSRESN DTIQSDTVRS SSKSDYFRIQ LNNQDYYMSK PTFLDPSHGE SLPLNQFSQ VPNIRVFGAL PTGHQVLCHV HGILPYMFIK YDGQITDTST LRHQRCAQVH KTLEVKIRAS FKRKKDDKHD L AGDKLGNL NFVADVSVVK GIPFYGYHVG WNLFYKISLL NPSCLSRISE LIRDGKIFGK KFEIYESHIP YLLQWTADFN LF GCSWINV DRCYFRSPVL NSILDIDKLT INDDLQLLLD RFCDFKCNVL SRRDFPRVGN GLIEIDILPQ FIKNREKLQH RDI HHDFLE KLGDISDIPV KPYVSSARDM INELTMQREE LSLKEYKEPP ETKRHVSGHQ WQSSGEFEAF YKKAQHKTST FDGQ IPNFE NFIDKNQKFS AINTPYEALP QLWPRLPQIE INNNSMQDKK NDDQVNASFT EYEICGVDNE NEGVKGSNIK SRSYS WLPE SIASPKDSTI LLDHQTKYHN TINFSMDCAM TQNMASKRKL RSSVSANKTS LLSRKRKKVM AAGLRYGKRA FVYGEP PFG YQDILNKLED EGFPKIDYKD PFFSNPVDLE NKPYAYAGKR FEISSTHVST RIPVQFGGET VSVYNKPTFD MFSSWKY AL KPPTYDAVQK WYNKVPSMGN KKTESQISMH TPHSKFLYKF ASDVSGKQKR KKSSVHDSLT HLTLEIHANT RSDKIPDP A IDEVSMIIWC LEEETFPLDL DIAYEGIMIV HKASEDSTFP TKIQHCINEI PVMFYESEFE MFEALTDLVL LLDPDILSG FEIHNFSWGY IIERCQKIHQ FDIVRELARV KCQIKTKLSD TWGYAHSSGI MITGRHMINI WRALRSDVNL TQYTIESAAF NILHKRLPH FSFESLTNMW NAKKSTTELK TVLNYWLSRA QINIQLLRKQ DYIARNIEQA RLIGIDFHSV YYRGSQFKVE S FLIRICKS ESFILLSPGK KDVRKQKALE CVPLVMEPES AFYKSPLIVL DFQSLYPSIM IGYNYCYSTM IGRVREINLT EN NLGVSKF SLPRNILALL KNDVTIAPNG VVYAKTSVRK STLSKMLTDI LDVRVMIKKT MNEIGDDNTT LKRLLNNKQL ALK LLANVT YGYTSASFSG RMPCSDLADS IVQTGRETLE KAIDIIEKDE TWNAKVVYGD TDSLFVYLPG KTAIEAFSIG HAMA ERVTQ NNPKPIFLKF EKVYHPSILI SKKRYVGFSY ESPSQTLPIF DAKGIETVRR DGIPAQQKII EKCIRLLFQT KDLSK IKKY LQNEFFKIQI GKVSAQDFCF AKEVKLGAYK SEKTAPAGAV VVKRRINEDH RAEPQYKERI PYLVVKGKQG QLLRER CVS PEEFLEGENL ELDSEYYINK ILIPPLDRLF NLIGINVGNW AQEIVKSKRA STTTTKVENI TRVGTSATCC NCGEELT KI CSLQLCDDCL EKRSTTTLSF LIKKLKRQKE YQTLKTVCRT CSYRYTSDAG IENDHIASKC NSYDCPVFYS RVKAERYL R DNQSVQREEA LISLNDW

UniProtKB: DNA polymerase zeta catalytic subunit

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Macromolecule #2: DNA polymerase zeta processivity subunit

MacromoleculeName: DNA polymerase zeta processivity subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 28.791654 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNRWVEKWLR VYLKCYINLI LFYRNVYPPQ SFDYTTYQSF NLPQFVPINR HPALIDYIEE LILDVLSKLT HVYRFSICII NKKNDLCIE KYVLDFSELQ HVDKDDQIIT ETEVFDEFRS SLNSLIMHLE KLPKVNDDTI TFEAVINAIE LELGHKLDRN R RVDSLEEK ...String:
MNRWVEKWLR VYLKCYINLI LFYRNVYPPQ SFDYTTYQSF NLPQFVPINR HPALIDYIEE LILDVLSKLT HVYRFSICII NKKNDLCIE KYVLDFSELQ HVDKDDQIIT ETEVFDEFRS SLNSLIMHLE KLPKVNDDTI TFEAVINAIE LELGHKLDRN R RVDSLEEK AEIERDSNWV KCQEDENLPD NNGFQPPKIK LTSLVGSDVG PLIIHQFSEK LISGDDKILN GVYSQYEEGE SI FGSLF

UniProtKB: DNA polymerase zeta processivity subunit

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Macromolecule #3: DNA polymerase delta small subunit

MacromoleculeName: DNA polymerase delta small subunit / type: protein_or_peptide / ID: 3 / 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 #4: DNA polymerase delta subunit 3

MacromoleculeName: DNA polymerase delta subunit 3 / type: protein_or_peptide / ID: 4 / 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 #5: DNA

MacromoleculeName: DNA / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.248954 KDa
SequenceString:
(DT)(DA)(DA)(DT)(DG)(DG)(DT)(DA)(DG)(DG) (DG)(DG)(DA)(DG)(DG)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DT)(DC)(DC)(DC)(DC)(DT)(DA) (DC)

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: DCP
Molecular weightTheoretical: 467.157 Da
Chemical component information

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 220 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

BufferpH: 7.8
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 71.63 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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156067
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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