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- EMDB-41371: Cryo-EM structure of the Rev1-Polzeta-DNA-dCTP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-41371
TitleCryo-EM structure of the Rev1-Polzeta-DNA-dCTP complex
Map data
Sample
  • Complex: 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
    • Protein or peptide: DNA repair protein REV1
    • DNA: DNA (30-MER)
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: water
KeywordsDNA repair / DNA replication / translesion DNA synthesis / DNA polymerase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Termination of translesion DNA synthesis / delta DNA polymerase complex / Translesion synthesis by POLK / Translesion synthesis by POLI / DNA amplification / deoxycytidyl transferase activity / Translesion synthesis by REV1 / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / DNA replication, removal of RNA primer ...Termination of translesion DNA synthesis / delta DNA polymerase complex / Translesion synthesis by POLK / Translesion synthesis by POLI / DNA amplification / deoxycytidyl transferase activity / Translesion synthesis by REV1 / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / DNA replication, removal of RNA primer / double-strand break repair via break-induced replication / lagging strand elongation / DNA metabolic process / leading strand elongation / error-free translesion synthesis / error-prone translesion synthesis / replication fork / nucleotide-excision repair / double-strand break repair via homologous recombination / base-excision repair / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 4 iron, 4 sulfur cluster binding / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin / mitochondrion / DNA binding / metal ion binding / nucleus / cytoplasm
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 / DNA repair protein Rev1 / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / 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 / DNA repair protein Rev1 / 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 / BRCT domain, a BRCA1 C-terminus 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 / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
POL31 isoform 1 / DNA repair protein REV1 / DNA polymerase zeta catalytic subunit / DNA polymerase zeta processivity subunit / DNA polymerase delta subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsMalik R / Aggarwal AK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35-GM131780 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Cryo-EM structure of the Rev1-Polζ holocomplex reveals the mechanism of their cooperativity in translesion DNA synthesis.
Authors: Radhika Malik / Robert E Johnson / Iban Ubarretxena-Belandia / Louise Prakash / Satya Prakash / Aneel K Aggarwal /
Abstract: Rev1-Polζ-dependent translesion synthesis (TLS) of DNA is crucial for maintaining genome integrity. To elucidate the mechanism by which the two polymerases cooperate in TLS, we determined the ...Rev1-Polζ-dependent translesion synthesis (TLS) of DNA is crucial for maintaining genome integrity. To elucidate the mechanism by which the two polymerases cooperate in TLS, we determined the cryogenic electron microscopic structure of the Saccharomyces cerevisiae Rev1-Polζ holocomplex in the act of DNA synthesis (3.53 Å). We discovered that a composite N-helix-BRCT module in Rev1 is the keystone of Rev1-Polζ cooperativity, interacting directly with the DNA template-primer and with the Rev3 catalytic subunit of Polζ. The module is positioned akin to the polymerase-associated domain in Y-family TLS polymerases and is set ideally to interact with PCNA. We delineate the full extent of interactions that the carboxy-terminal domain of Rev1 makes with Polζ and identify potential new druggable sites to suppress chemoresistance from first-line chemotherapeutics. Collectively, our results provide fundamental new insights into the mechanism of cooperativity between Rev1 and Polζ in TLS.
History
DepositionJul 27, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41371.png

Downloads & links

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Map

FileDownload / File: emd_41371.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.069 Å
Density
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.3736604 - 3.9784222
Average (Standard dev.)0.0042638956 (±0.07169006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 307.872 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41371_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41371_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA complex

EntireName: DNA complex
Components
  • Complex: 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
    • Protein or peptide: DNA repair protein REV1
    • DNA: DNA (30-MER)
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: water

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Supramolecule #1: DNA complex

SupramoleculeName: DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
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 (brewer's yeast)
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 (brewer's yeast)
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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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: POL31 isoform 1

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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 (brewer's yeast)
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 repair protein REV1

MacromoleculeName: DNA repair protein REV1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 112.384219 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGEHGGLVDL LDSDLEYSIN RETPDKNNCL SQQSVNDSHL TAKTGGLNAR SFLSTLSDDS LIEYVNQLSQ TNKNNSNPTA GTLRFTTKN ISCDELHADL GGGEDSPIAR SVIEIQESDS NGDDVKKNTV YTREAYFHEK AHGQTLQDQI LKDQYKDQIS S QSSKIFKN ...String:
MGEHGGLVDL LDSDLEYSIN RETPDKNNCL SQQSVNDSHL TAKTGGLNAR SFLSTLSDDS LIEYVNQLSQ TNKNNSNPTA GTLRFTTKN ISCDELHADL GGGEDSPIAR SVIEIQESDS NGDDVKKNTV YTREAYFHEK AHGQTLQDQI LKDQYKDQIS S QSSKIFKN CVIYINGYTK PGRLQLHEMI VLHGGKFLHY LSSKKTVTHI VASNLPLKKR IEFANYKVVS PDWIVDSVKE AR LLPWQNY SLTSKLDEQQ KKLDNCKTVN SIPLPSETSL HKGSKCVGSA LLPVEQQSPV NLNNLEAKRI VACDDPDFLT SYF AHSRLH HLSAWKANLK DKFLNENIHK YTKITDKDTY IIFHIDFDCF FATVAYLCRS SSFSACDFKR DPIVVCHGTK NSDI ASCNY VARSYGIKNG MWVSQAEKML PNGIKLISLP YTFEQFQLKS EAFYSTLKRL NIFNLILPIS IDEAVCVRII PDNIH NTNT LNARLCEEIR QEIFQGTNGC TVSIGCSDSL VLARLALKMA KPNGYNITFK SNLSEEFWSS FKLDDLPGVG HSTLSR LES TFDSPHSLND LRKRYTLDAL KASVGSKLGM KIHLALQGQD DEESLKILYD PKEVLQRKSL SIDINWGIRF KNITQVD LF IERGCQYLLE KLNEINKTTS QITLKLMRRC KDAPIEPPKY MGMGRCDSFS RSSRLGIPTN EFGIIATEMK SLYRTLGC P PMELRGLALQ FNKLVDVGPD NNQLKLRLPF KTIVTNRAFE ALPEDVKNDI NNEFEKRNYK RKESGLTSNS LSSKKKGFA ISRLEVNDLP STMEEQFMNE LPTQIRAEVR HDLRIQKKIQ QTKLGNLQEK IKRREESLQN EKNHFMGQNS IFQPIKFQNL TRFKKICQL VKQWVAETLG DGGPHEKDVK LFVKYLIKLC DSNRVHLVLH LSNLISRELN LCAFLNQDHS GFQTWERILL N DIIPLLNR NKHTYQTVRK LDMDFEV

UniProtKB: DNA repair protein REV1

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Macromolecule #6: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 6 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: DNA molecule (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 #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / 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 / Deoxycytidine triphosphate

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / 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 #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 43 / 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

BufferpH: 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.19 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153551

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