+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14080 | |||||||||
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Title | complex of DNA ligase I and FEN1 on PCNA and DNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA / Replication / Complex / Ligase / PCNA / Ligation / FEN1 / Flap Endonuclease I / Okazaki fragment maturation | |||||||||
Function / homology | Function and homology information Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / DNA ligase activity / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex ...Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / DNA ligase activity / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / DNA ligase (ATP) / mitotic telomere maintenance via semi-conservative replication / nucleic acid metabolic process / DNA ligase (ATP) activity / purine-specific mismatch base pair DNA N-glycosylase activity / 5'-flap endonuclease activity / nuclear lamina / MutLalpha complex binding / DNA replication, removal of RNA primer / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / 5'-3' exonuclease activity / UV protection / DNA ligation / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / replisome / exonuclease activity / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / DNA biosynthetic process / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / Early Phase of HIV Life Cycle / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mismatch repair / translesion synthesis / cyclin-dependent protein kinase holoenzyme complex / DNA polymerase binding / response to cadmium ion / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / replication fork / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / memory / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / double-strand break repair / RNA-DNA hybrid ribonuclease activity / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA recombination / DNA replication / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / nuclear body / cell division Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Blair K / Tehseen M / Raducanu VS / Shahid T / Lancey C / Cruehet R / Hamdan S / De Biasio A | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing. Authors: Kerry Blair / Muhammad Tehseen / Vlad-Stefan Raducanu / Taha Shahid / Claudia Lancey / Fahad Rashid / Ramon Crehuet / Samir M Hamdan / Alfredo De Biasio / Abstract: During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present ...During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIP) and DNA binding domain (PIP). Once Lig1 and PCNA assemble as two-stack rings encircling DNA, PIP is released from PCNA and only PIP is required for ligation to facilitate the substrate handoff from FEN1. Consistently, we observed that PCNA forms a defined complex with FEN1 and nicked DNA, and it recruits Lig1 to an unoccupied monomer creating a toolbelt that drives the transfer of DNA to Lig1. Collectively, our results provide a structural model on how PCNA regulates FEN1 and Lig1 during Okazaki fragments maturation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14080.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-14080-v30.xml emd-14080.xml | 23.9 KB 23.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14080_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_14080.png | 85.5 KB | ||
Filedesc metadata | emd-14080.cif.gz | 7.4 KB | ||
Others | emd_14080_half_map_1.map.gz emd_14080_half_map_2.map.gz | 50.8 MB 50.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14080 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14080 | HTTPS FTP |
-Validation report
Summary document | emd_14080_validation.pdf.gz | 844.8 KB | Display | EMDB validaton report |
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Full document | emd_14080_full_validation.pdf.gz | 844.3 KB | Display | |
Data in XML | emd_14080_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_14080_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14080 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14080 | HTTPS FTP |
-Related structure data
Related structure data | 7qo1MC 7qnzC 8b8tC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14080.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_14080_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14080_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : complex of DNA ligase I and FEN1 on PCNA and DNA
Entire | Name: complex of DNA ligase I and FEN1 on PCNA and DNA |
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Components |
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-Supramolecule #1: complex of DNA ligase I and FEN1 on PCNA and DNA
Supramolecule | Name: complex of DNA ligase I and FEN1 on PCNA and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #6, #1, #3, #5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA ligase 1
Macromolecule | Name: DNA ligase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA ligase (ATP) |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 84.248555 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: CKESLTEAEV ATEKEGEDGD QPTTPPKPLK TSKAETPTES VSEPEVATKQ ELQEEEEQTK PPRRAPKTLS SFFTPRKPAV KKEVKEEEP GAPGKEGAAE GPLDPSGYNP AKNNYHPVED ACWKPGQKVP YLAVARTFEK IEEVSARLRM VETLSNLLRS V VALSPPDL ...String: CKESLTEAEV ATEKEGEDGD QPTTPPKPLK TSKAETPTES VSEPEVATKQ ELQEEEEQTK PPRRAPKTLS SFFTPRKPAV KKEVKEEEP GAPGKEGAAE GPLDPSGYNP AKNNYHPVED ACWKPGQKVP YLAVARTFEK IEEVSARLRM VETLSNLLRS V VALSPPDL LPVLYLSLNH LGPPQQGLEL GVGDGVLLKA VAQATGRQLE SVRAEAAEKG DVGLVAENSR STQRLMLPPP PL TASGVFS KFRDIARLTG SASTAKKIDI IKGLFVACRH SEARFIARSL SGRLRLGLAE QSVLAALSQA VSLTPPGQEF PPA MVDAGK GKTAEARKTW LEEQGMILKQ TFCEVPDLDR IIPVLLEHGL ERLPEHCKLS PGIPLKPMLA HPTRGISEVL KRFE EAAFT CEYKYDGQRA QIHALEGGEV KIFSRNQEDN TGKYPDIISR IPKIKLPSVT SFILDTEAVA WDREKKQIQP FQVLT TRKR KEVDASEIQV QVCLYAFDLI YLNGESLVRE PLSRRRQLLR ENFVETEGEF VFATSLDTKD IEQIAEFLEQ SVKDSC EGL MVKTLDVDAT YEIAKRSHNW LKLKKDYLDG VGDTLDLVVI GAYLGRGKRA GRYGGFLLAS YDEDSEELQA ICKLGTG FS DEELEEHHQS LKALVLPSPR PYVRIDGAVI PDHWLDPSAV WEVKCADLSL SPIYPAARGL VDSDKGISLR FPRFIRVR E DKQPEQATTS AQVACLYRKQ SQIQNQQGED SGSDPEDTY UniProtKB: DNA ligase 1 |
-Macromolecule #2: Proliferating cell nuclear antigen
Macromolecule | Name: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.088061 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GPHMFEARLV QGSILKKVLE ALKDLINEAC WDISSSGVNL QSMDSSHVSL VQLTLRSEGF DTYRCDRNLA MGVNLTSMSK ILKCAGNED IITLRAEDNA DTLALVFEAP NQEKVSDYEM KLMDLDVEQL GIPEQEYSCV VKMPSGEFAR ICRDLSHIGD A VVISCAKD ...String: GPHMFEARLV QGSILKKVLE ALKDLINEAC WDISSSGVNL QSMDSSHVSL VQLTLRSEGF DTYRCDRNLA MGVNLTSMSK ILKCAGNED IITLRAEDNA DTLALVFEAP NQEKVSDYEM KLMDLDVEQL GIPEQEYSCV VKMPSGEFAR ICRDLSHIGD A VVISCAKD GVKFSASGEL GNGNIKLSQT SNVDKEEEAV TIEMNEPVQL TFALRYLNFF TKATPLSSTV TLSMSADVPL VV EYKIADM GHLKYYLAPK IEDEEGS UniProtKB: Proliferating cell nuclear antigen |
-Macromolecule #6: Flap endonuclease 1
Macromolecule | Name: Flap endonuclease 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.617039 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGIQGLAKLI ADVAPSAIRE NDIKSYFGRK VAIDASMSIY QFLIAVRQGG DVLQNEEGET TSHLMGMFYR TIRMMENGIK PVYVFDGKP PQLKSGELAK RSERRAEAEK QLQQAQAAGA EQEVEKFTKR LVKVTKQHND ECKHLLSLMG IPYLDAPSEA E ASCAALVK ...String: MGIQGLAKLI ADVAPSAIRE NDIKSYFGRK VAIDASMSIY QFLIAVRQGG DVLQNEEGET TSHLMGMFYR TIRMMENGIK PVYVFDGKP PQLKSGELAK RSERRAEAEK QLQQAQAAGA EQEVEKFTKR LVKVTKQHND ECKHLLSLMG IPYLDAPSEA E ASCAALVK AGKVYAAATE DMACLTFGSP VLMRHLTASE AKKLPIQEFH LSRILQELGL NQEQFVDLCI LLGSDYCESI RG IGPKRAV DLIQKHKSIE EIVRRLDPNK YPVPENWLHK EAHQLFLEPE VLDPESVELK WSEPNEEELI KFMCGEKQFS EER IRSGVK RLSKSRQGST QGRLDDFFKV TGSLSSAKRK EPEPKGSTKK KAKTGAAGKF KRGK UniProtKB: Flap endonuclease 1 |
-Macromolecule #3: Oligo19ddC
Macromolecule | Name: Oligo19ddC / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 5.802744 KDa |
Sequence | String: (DG)(DC)(DT)(DT)(DC)(DT)(DG)(DT)(DG)(DC) (DT)(DG)(DA)(DT)(DG)(DC)(DG)(DT)(DOC) |
-Macromolecule #4: Oligo13P
Macromolecule | Name: Oligo13P / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.976599 KDa |
Sequence | String: (DG)(DT)(DC)(DG)(DG)(DA)(DC)(DT)(DG)(DA) (DA)(DC)(DC) |
-Macromolecule #5: Oligo32
Macromolecule | Name: Oligo32 / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.845345 KDa |
Sequence | String: (DG)(DG)(DT)(DT)(DC)(DA)(DG)(DT)(DC)(DC) (DG)(DA)(DC)(DG)(DA)(DC)(DG)(DC)(DA)(DT) (DC)(DA)(DG)(DC)(DA)(DC)(DA)(DG)(DA) (DA)(DG)(DC) |
-Macromolecule #7: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ChemComp-AMP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. Details: The grid was coated with graphene oxide prior to use. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 18.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7qo1: |