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- EMDB-44357: Human polymerase epsilon bound to PCNA and DNA in the nucleotide ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44357
TitleHuman polymerase epsilon bound to PCNA and DNA in the nucleotide exchange state
Map dataFinal EM map
Sample
  • Complex: The DNA bound Pol epsilon and PCNA complex
    • Protein or peptide: DNA polymerase epsilon catalytic subunit A
    • Protein or peptide: Proliferating cell nuclear antigen
    • DNA: DNA (5'-D(P*GP*TP*GP*AP*TP*GP*CP*TP*TP*TP*AP*GP*AP*TP*TP*TP*TP*TP*C)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*GP*TP*GP*AP*AP*AP*AP*AP*TP*CP*TP*AP*AP*AP*GP*CP*AP*TP*CP*AP*C)-3')
  • Ligand: IRON/SULFUR CLUSTER
KeywordsDNA polymerase / DNA / DNA Binding Protein-DNA complex
Function / homology
Function and homology information


DNA replication initiation / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / epsilon DNA polymerase complex / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / MutLalpha complex binding / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity ...DNA replication initiation / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / epsilon DNA polymerase complex / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / MutLalpha complex binding / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / DNA replication proofreading / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / response to L-glutamate / histone acetyltransferase binding / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / replication fork processing / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / mismatch repair / embryonic organ development / translesion synthesis / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / epithelial cell differentiation / base-excision repair, gap-filling / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / male germ cell nucleus / replication fork / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / DNA-templated DNA replication / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / G1/S transition of mitotic cell cycle / cellular response to UV / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / heart development / 4 iron, 4 sulfur cluster binding / DNA replication / damaged DNA binding / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / nucleotide binding / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA ...DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / 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, 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
Proliferating cell nuclear antigen / DNA polymerase epsilon catalytic subunit A
Similarity search - Component
Biological speciesHomo sapiens (human) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.01 Å
AuthorsWang F / He Q / Li H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM148159 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structures of the human leading strand Polε-PCNA holoenzyme.
Authors: Qing He / Feng Wang / Nina Y Yao / Michael E O'Donnell / Huilin Li /
Abstract: In eukaryotes, the leading strand DNA is synthesized by Polε and the lagging strand by Polδ. These replicative polymerases have higher processivity when paired with the DNA clamp PCNA. While the ...In eukaryotes, the leading strand DNA is synthesized by Polε and the lagging strand by Polδ. These replicative polymerases have higher processivity when paired with the DNA clamp PCNA. While the structure of the yeast Polε catalytic domain has been determined, how Polε interacts with PCNA is unknown in any eukaryote, human or yeast. Here we report two cryo-EM structures of human Polε-PCNA-DNA complex, one in an incoming nucleotide bound state and the other in a nucleotide exchange state. The structures reveal an unexpected three-point interface between the Polε catalytic domain and PCNA, with the conserved PIP (PCNA interacting peptide)-motif, the unique P-domain, and the thumb domain each interacting with a different protomer of the PCNA trimer. We propose that the multi-point interface prevents other PIP-containing factors from recruiting to PCNA while PCNA functions with Polε. Comparison of the two states reveals that the finger domain pivots around the [4Fe-4S] cluster-containing tip of the P-domain to regulate nucleotide exchange and incoming nucleotide binding.
History
DepositionMar 31, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44357.png

Downloads & links

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Map

FileDownload / File: emd_44357.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.28685215 - 0.54816604
Average (Standard dev.)0.0002940317 (±0.012837055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened EM map

Fileemd_44357_additional_1.map
AnnotationUnsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_44357_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_44357_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : The DNA bound Pol epsilon and PCNA complex

EntireName: The DNA bound Pol epsilon and PCNA complex
Components
  • Complex: The DNA bound Pol epsilon and PCNA complex
    • Protein or peptide: DNA polymerase epsilon catalytic subunit A
    • Protein or peptide: Proliferating cell nuclear antigen
    • DNA: DNA (5'-D(P*GP*TP*GP*AP*TP*GP*CP*TP*TP*TP*AP*GP*AP*TP*TP*TP*TP*TP*C)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*GP*TP*GP*AP*AP*AP*AP*AP*TP*CP*TP*AP*AP*AP*GP*CP*AP*TP*CP*AP*C)-3')
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: The DNA bound Pol epsilon and PCNA complex

SupramoleculeName: The DNA bound Pol epsilon and PCNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: DNA polymerase epsilon catalytic subunit A

MacromoleculeName: DNA polymerase epsilon catalytic subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 261.753234 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MSLRSGGRRR ADPGADGEAS RDDGATSSVS ALKRLERSQW TDKMDLRFGF ERLKEPGEKT GWLINMHPTE ILDEDKRLGS AVDYYFIQD DGSRFKVALP YKPYFYIATR KGCEREVSSF LSKKFQGKIA KVETVPKEDL DLPNHLVGLK RNYIRLSFHT V EDLVKVRK ...String:
MSLRSGGRRR ADPGADGEAS RDDGATSSVS ALKRLERSQW TDKMDLRFGF ERLKEPGEKT GWLINMHPTE ILDEDKRLGS AVDYYFIQD DGSRFKVALP YKPYFYIATR KGCEREVSSF LSKKFQGKIA KVETVPKEDL DLPNHLVGLK RNYIRLSFHT V EDLVKVRK EISPAVKKNR EQDHASDAYT ALLSSVLQRG GVITDEEETS KKIADQLDNI VDMREYDVPY HIRLSIDLKI HV AHWYNVR YRGNAFPVEI TRRDDLVERP DPVVLAFAIA TTKLPLKFPD AETDQIMMIS YMIDGQGYLI TNREIVSEDI EDF EFTPKP EYEGPFCVFN EPDEAHLIQR WFEHVQETKP TIMVTYNGDF FDWPFVEARA AVHGLSMQQE IGFQKDSQGE YKAP QCIHM DCLRWVKRDS YLPVGSHNLK AAAKAKLGYD PVELDPEDMC RMATEQPQTL ATYSVSDAVA TYYLYMKYVH PFIFA LCTI IPMEPDEVLR KGSGTLCEAL LMVQAFHANI IFPNKQEQEF NKLTDDGHVL DSETYVGGHV EALESGVFRS DIPCRF RMN PAAFDFLLQR VEKTLRHALE EEEKVPVEQV TNFEEVCDEI KSKLASLKDV PSRIECPLIY HLDVGAMYPN IILTNRL QP SAMVDEATCA ACDFNKPGAN CQRKMAWQWR GEFMPASRSE YHRIQHQLES EKFPPLFPEG PARAFHELSR EEQAKYEK R RLADYCRKAY KKIHITKVEE RLTTICQREN SFYVDTVRAF RDRRYEFKGL HKVWKKKLSA AVEVGDAAEV KRCKNMEVL YDSLQLAHKC ILNSFYGYVM RKGARWYSME MAGIVCFTGA NIITQARELI EQIGRPLELD TDGIWCVLPN SFPENFVFKT TNVKKPKVT ISYPGAMLNI MVKEGFTNDQ YQELAEPSSL TYVTRSENSI FFEVDGPYLA MILPASKEEG KKLKKRYAVF N EDGSLAEL KGFEVKRRGE LQLIKIFQSS VFEAFLKGST LEEVYGSVAK VADYWLDVLY SKAANMPDSE LFELISENRS MS RKLEDYG EQKSTSISTA KRLAEFLGDQ MVKDAGLSCR YIISRKPEGS PVTERAIPLA IFQAEPTVRK HFLRKWLKSS SLQ DFDIRA ILDWDYYIER LGSAIQKIIT IPAALQQVKN PVPRVKHPDW LHKKLLEKND VYKQKKISEL FTLEGRRQVT MAEA SEDSP RPSAPDMEDF GLVKLPHPAA PVTVKRKRVL WESQEESQDL TPTVPWQEIL GQPPALGTSQ EEWLVWLRFH KKKWQ LQAR QRLARRKRQR LESAEGVLRP GAIRDGPATG LGSFLRRTAR SILDLPWQIV QISETSQAGL FRLWALVGSD LHCIRL SIP RVFYVNQRVA KAEEGASYRK VNRVLPRSNM VYNLYEYSVP EDMYQEHINE INAELSAPDI EGVYETQVPL LFRALVH LG CVCVVNKQLV RHLSGWEAET FALEHLEMRS LAQFSYLEPG SIRHIYLYHH AQAHKALFGI FIPSQRRASV FVLDTVRS N QMPSLGALYS AEHGLLLEKV GPELLPPPKH TFEVRAETDL KTICRAIQRF LLAYKEERRG PTLIAVQSSW ELKRLASEI PVLEEFPLVP ICVADKINYG VLDWQRHGAR RMIRHYLNLD TCLSQAFEMS RYFHIPIGNL PEDISTFGSD LFFARHLQRH NHLLWLSPT ARPDLGGKEA DDNCLVMEFD DQATVEINSS GCYSTVCVEL DLQNLAVNTI LQSHHVNDME GADSMGISFD V IQQASLED MITGGQAASA PASYDETALC SNTFRILKSM VVGWVKEITQ YHNIYADNQV MHFYRWLRSP SSLLHDPALH RT LHNMMKK LFLQLIAEFK RLGSSVIYAN FNRIILCTKK RRVEDAIAYV EYITSSIHSK ETFHSLTISF SRCWEFLLWM DPS NYGGIK GKVSSRIHCG LQDSQKAGGA EDEQENEDDE EERDGEEEEE AEESNVEDLL ENNWNILQFL PQAASCQNYF LMIV SAYIV AVYHCMKDGL RRSAPGSTPV RRRGASQLSQ EAEGAVGALP GMITFSQDYV ANELTQSFFT ITQKIQKKVT GSRNS TELS EMFPVLPGSH LLLNNPALEF IKYVCKVLSL DTNITNQVNK LNRDLLRLVD VGEFSEEAQF RDPCRSYVLP EVICRS CNF CRDLDLCKDS SFSEDGAVLP QWLCSNCQAP YDSSAIEMTL VEVLQKKLMA FTLQDLVCLK CRGVKETSMP VYCSCAG DF ALTIHTQVFM EQIGIFRNIA QHYGMSYLLE TLEWLLQKNP QLGH

UniProtKB: DNA polymerase epsilon catalytic subunit A

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Macromolecule #2: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.795752 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK ...String:
MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK FSASGELGNG NIKLSQTSNV DKEEEAVTIE MNEPVQLTFA LRYLNFFTKA TPLSSTVTLS MSADVPLVVE YK IADMGHL KYYLAPKIED EEGS

UniProtKB: Proliferating cell nuclear antigen

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Macromolecule #3: DNA (5'-D(P*GP*TP*GP*AP*TP*GP*CP*TP*TP*TP*AP*GP*AP*TP*TP*TP*TP*TP...

MacromoleculeName: DNA (5'-D(P*GP*TP*GP*AP*TP*GP*CP*TP*TP*TP*AP*GP*AP*TP*TP*TP*TP*TP*C)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 10.823965 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DG)(DT)(DT)(DC)(DA)(DG) (DC)(DA)(DA)(DG)(DG)(DT)(DG)(DA)(DT)(DG) (DC)(DT)(DT)(DT)(DA)(DG)(DA)(DT)(DT) (DT)(DT)(DT)(DC)(DA)(DC)

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Macromolecule #4: DNA (5'-D(P*AP*AP*AP*GP*TP*GP*AP*AP*AP*AP*AP*TP*CP*TP*AP*AP*AP*GP...

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*GP*TP*GP*AP*AP*AP*AP*AP*TP*CP*TP*AP*AP*AP*GP*CP*AP*TP*CP*AP*C)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 18.13668 KDa
SequenceString: (DG)(DC)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DA) (DG)(DA)(DG)(DC)(DC)(DA)(DG)(DC)(DA)(DG) (DC)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DA) (DA)(DA)(DA)(DT)(DC)(DT)(DA)(DA)(DA)(DG) (DC) (DA)(DT)(DC)(DA)(DC)(DC) ...String:
(DG)(DC)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DA) (DG)(DA)(DG)(DC)(DC)(DA)(DG)(DC)(DA)(DG) (DC)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DA) (DA)(DA)(DA)(DT)(DC)(DT)(DA)(DA)(DA)(DG) (DC) (DA)(DT)(DC)(DA)(DC)(DC)(DT)(DT) (DG)(DC)(DT)(DG)(DA)(DA)(DC)(DC)(DT)(DC) (DA)

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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

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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

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClSodium chloride
1.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71210
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9b8s:
Human polymerase epsilon bound to PCNA and DNA in the nucleotide exchange state

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