+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41663 | ||||||||||||
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Title | Cryo-EM structure of S. cerevisiae PolE-Ctf18-8-1-DNA | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Pol2 / Ctf18-8-1 / DNA / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / Ctf18 RFC-like complex / telomere tethering at nuclear periphery / maintenance of DNA trinucleotide repeats / SUMO binding / Activation of the pre-replicative complex / nucleotide-excision repair, DNA gap filling ...maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / epsilon DNA polymerase complex / Ctf18 RFC-like complex / telomere tethering at nuclear periphery / maintenance of DNA trinucleotide repeats / SUMO binding / Activation of the pre-replicative complex / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / leading strand elongation / nuclear replication fork / Dual incision in TC-NER / chromosome, centromeric region / DNA replication initiation / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / double-strand break repair via homologous recombination / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / mRNA binding / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Yuan Z / Georgescu R / O'Donnell M / Li H | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2024 Title: Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis. Authors: Zuanning Yuan / Roxana Georgescu / Nina Y Yao / Olga Yurieva / Michael E O'Donnell / Huilin Li / Abstract: The proliferating cell nuclear antigen (PCNA) clamp encircles DNA to hold DNA polymerases (Pols) to DNA for processivity. The Ctf18-RFC PCNA loader, a replication factor C (RFC) variant, is specific ...The proliferating cell nuclear antigen (PCNA) clamp encircles DNA to hold DNA polymerases (Pols) to DNA for processivity. The Ctf18-RFC PCNA loader, a replication factor C (RFC) variant, is specific to the leading-strand Pol (Polε). We reveal here the underlying mechanism of Ctf18-RFC specificity to Polε using cryo-electron microscopy and biochemical studies. We found that both Ctf18-RFC and Polε contain specific structural features that direct PCNA loading onto DNA. Unlike other clamp loaders, Ctf18-RFC has a disordered ATPase associated with a diverse cellular activities (AAA+) motor that requires Polε to bind and stabilize it for efficient PCNA loading. In addition, Ctf18-RFC can pry prebound Polε off of DNA, then load PCNA onto DNA and transfer the PCNA-DNA back to Polε. These elements in both Ctf18-RFC and Polε provide specificity in loading PCNA onto DNA for Polε. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41663.map.gz | 10.5 MB | EMDB map data format | |
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Header (meta data) | emd-41663-v30.xml emd-41663.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
Images | emd_41663.png | 199.7 KB | ||
Filedesc metadata | emd-41663.cif.gz | 7.8 KB | ||
Others | emd_41663_half_map_1.map.gz emd_41663_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41663 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41663 | HTTPS FTP |
-Validation report
Summary document | emd_41663_validation.pdf.gz | 928.8 KB | Display | EMDB validaton report |
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Full document | emd_41663_full_validation.pdf.gz | 928.4 KB | Display | |
Data in XML | emd_41663_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_41663_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41663 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41663 | HTTPS FTP |
-Related structure data
Related structure data | 8tw9M 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_41663.map.gz / Format: CCP4 / Size: 64 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: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41663_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41663_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ctf18-RFC-PCNA complex
Entire | Name: Ctf18-RFC-PCNA complex |
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Components |
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-Supramolecule #1: Ctf18-RFC-PCNA complex
Supramolecule | Name: Ctf18-RFC-PCNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Chromosome transmission fidelity protein 18
Macromolecule | Name: Chromosome transmission fidelity protein 18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 3.171607 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: TVKIWVKYNE GFSNAVRKNV TWNNLW UniProtKB: Chromosome transmission fidelity protein 18 |
-Macromolecule #4: DNA polymerase epsilon catalytic subunit A
Macromolecule | Name: DNA polymerase epsilon catalytic subunit A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 255.992484 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MMFGKKKNNG GSSTARYSAG NKYNTLSNNY ALSAQQLLNA SKIDDIDSMM GFERYVPPQY NGRFDAKDID QIPGRVGWLT NMHATLVSQ ETLSSGSNGG GNSNDGERVT TNQGISGVDF YFLDEEGGSF KSTVVYDPYF FIACNDESRV NDVEELVKKY L ESCLKSLQ ...String: MMFGKKKNNG GSSTARYSAG NKYNTLSNNY ALSAQQLLNA SKIDDIDSMM GFERYVPPQY NGRFDAKDID QIPGRVGWLT NMHATLVSQ ETLSSGSNGG GNSNDGERVT TNQGISGVDF YFLDEEGGSF KSTVVYDPYF FIACNDESRV NDVEELVKKY L ESCLKSLQ IIRKEDLTMD NHLLGLQKTL IKLSFVNSNQ LFEARKLLRP ILQDNANNNV QRNIYNVAAN GSEKVDAKHL IE DIREYDV PYHVRVSIDK DIRVGKWYKV TQQGFIEDTR KIAFADPVVM AFDIETTKPP LKFPDSAVDQ IMMISYMIDG EGF LITNRE IISEDIEDFE YTPKPEYPGF FTIFNENDEV ALLQRFFEHI RDVRPTVIST FNGDFFDWPF IHNRSKIHGL DMFD EIGFA PDAEGEYKSS YCSHMDCFRW VKRDSYLPQG SQGLKAVTQS KLGYNPIELD PELMTPYAFE KPQHLSEYSV SDAVA TYYL YMKYVHPFIF SLCTIIPLNP DETLRKGTGT LCEMLLMVQA YQHNILLPNK HTDPIERFYD GHLLESETYV GGHVES LEA GVFRSDLKNE FKIDPSAIDE LLQELPEALK FSVEVENKSS VDKVTNFEEI KNQITQKLLE LKENNIRNEL PLIYHVD VA SMYPNIMTTN RLQPDSIKAE RDCASCDFNR PGKTCARKLK WAWRGEFFPS KMDEYNMIKR ALQNETFPNK NKFSKKKV L TFDELSYADQ VIHIKKRLTE YSRKVYHRVK VSEIVEREAI VCQRENPFYV DTVKSFRDRR YEFKGLAKTW KGNLSKIDP SDKHARDEAK KMIVLYDSLQ LAHKVILNSF YGYVMRKGSR WYSMEMAGIT CLTGATIIQM ARALVERVGR PLELDTDGIW CILPKSFPE TYFFTLENGK KLYLSYPCSM LNYRVHQKFT NHQYQELKDP LNYIYETHSE NTIFFEVDGP YKAMILPSSK E EGKGIKKR YAVFNEDGSL AELKGFELKR RGELQLIKNF QSDIFKVFLE GDTLEGCYSA VASVCNRWLD VLDSHGLMLE DE DLVSLIC ENRSMSKTLK EYEGQKSTSI TTARRLGDFL GEDMVKDKGL QCKYIISSKP FNAPVTERAI PVAIFSADIP IKR SFLRRW TLDPSLEDLD IRTIIDWGYY RERLGSAIQK IITIPAALQG VSNPVPRVEH PDWLKRKIAT KEDKFKQTSL TKFF SKTKN VPTMGKIKDI EDLFEPTVEE DNAKIKIART TKKKAVSKRK RNQLTNEEDP LVLPSEIPSM DEDYVGWLNY QKIKW KIQA RDRKRRDQLF GNTNSSRERS ALGSMIRKQA ESYANSTWEV LQYKDSGEPG VLEVFVTING KVQNITFHIP KTIYMK FKS QTMPLQKIKN CLIEKSSASL PNNPKTSNPA GGQLFKITLP ESVFLEEKEN CTSIFNDENV LGVFEGTITP HQRAIMD LG ASVTFRSKAM GALGKGIQQG FEMKDLSMAE NERYLSGFSM DIGYLLHFPT SIGYEFFSLF KSWGDTITIL VLKPSNQA Q EINASSLGQI YKQMFEKKKG KIETYSYLVD IKEDINFEFV YFTDISKLYR RLSQETTKLK EERGLQFLLL LQSPFITKL LGTIRLLNQM PIVKLSLNEV LLPQLNWQPT LLKKLVNHVL SSGSWISHLI KLSQYSNIPI CNLRLDSMDY IIDVLYARKL KKENIVLWW NEKAPLPDHG GIQNDFDLNT SWIMNDSEFP KINNSGVYDN VVLDVGVDNL TVNTILTSAL INDAEGSDLV N NNMGIDDK DAVINSPSEF VHDAFSNDAL NVLRGMLKEW WDEALKENST ADLLVNSLAS WVQNPNAKLF DGLLRYHVHN LT KKALLQL VNEFSALGST IVYADRNQIL IKTNKYSPEN CYAYSQYMMK AVRTNPMFSY LDLNIKRYWD LLIWMDKFNF SGL ACIEIE EKENQDYTAV SQWQLKKFLS PIYQPEFEDW MMIILDSMLK TKQSYLKLNS GTQRPTQIVN VKKQDKEDSV ENSL NGFSH LFSKPLMKRV KKLFKNQQEF ILDPQYEADY VIPVLPGSHL NVKNPLLELV KSLCHVMLLS KSTILEIRTL RKELL KIFE LREFAKVAEF KDPSLSLVVP DFLCEYCFFI SDIDFCKAAP ESIFSCVRCH KAFNQVLLQE HLIQKLRSDI ESYLIQ DLR CSRCHKVKRD YMSAHCPCAG AWEGTLPRES IVQKLNVFKQ VAKYYGFDIL LSCIADLTI UniProtKB: DNA polymerase epsilon catalytic subunit A |
-Macromolecule #5: Chromosome transmission fidelity protein 8
Macromolecule | Name: Chromosome transmission fidelity protein 8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 15.058493 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: PSVDIDASQW QKLTQSREKQ TTVITPLGMM MLEIQGELEL PKDFASLARR DSPNEGRFSE QDGETLIRFG SLQIDGERAT LFVGKKQRL LGKVTKLDVP MGIMHFNSKD NKVELVDVMK YKVIFKDRPL PIM UniProtKB: Chromosome transmission fidelity protein 8 |
-Macromolecule #6: Sister chromatid cohesion protein DCC1
Macromolecule | Name: Sister chromatid cohesion protein DCC1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 44.133785 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSINLHSAPE YDPSYKLIQL TPELLDIIQD PVQNHQLRFK SLDKDKSEVV LCSHDKTWVL KQRKHSNTVL LMREFVPEQP ITFDETLLF GLSKPYMDVV GFAKTESEFE TRETHGELNL NSVPIYNGEL DFSDKIMKRS STKVIGTLEE LLENSPCSAL E GISKWHKI ...String: MSINLHSAPE YDPSYKLIQL TPELLDIIQD PVQNHQLRFK SLDKDKSEVV LCSHDKTWVL KQRKHSNTVL LMREFVPEQP ITFDETLLF GLSKPYMDVV GFAKTESEFE TRETHGELNL NSVPIYNGEL DFSDKIMKRS STKVIGTLEE LLENSPCSAL E GISKWHKI GGSVKDGVLC ILSQDFLFKA LHVLLMSAMA ESLDLQHLNV EDTHHAVGKD IEDEFNPYTR EIIETVLNKF AV QEQEAEN NTWRLRIPFI AQWYGIQALR KYVSGISMPI DEFLIKWKSL FPPFFPCDID IDMLRGYHFK PTDKTVQYIA KST LPMDPK ERFKVLFRLQ SQWDLEDIKP LIEELNSRGM KIDSFIMKYA RRKRLGKKTV VTSR UniProtKB: Sister chromatid cohesion protein DCC1 |
-Macromolecule #2: Primer DNA
Macromolecule | Name: Primer DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 2.737795 KDa |
Sequence | String: (DT)(DG)(DT)(DT)(DG)(DC)(DT)(DG)(DC) |
-Macromolecule #3: Template DNA
Macromolecule | Name: Template DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.567998 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(DA)(DG) (DC)(DA)(DA)(DC)(DA) |
-Macromolecule #7: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 385806 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |