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- EMDB-41664: Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-41664
TitleCryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex
Map data
Sample
  • Complex: Ctf18-RFC-PCNA-PolE-DNA complex
    • Protein or peptide: x 10 types
    • DNA: x 2 types
  • Ligand: x 4 types
KeywordsCtf18 / RFC2-5 / PCNA / Pol2 / DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / DNA clamp unloading / Rad17 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic mismatch repair / epsilon DNA polymerase complex / Processive synthesis on the lagging strand ...maintenance of mitotic sister chromatid cohesion / gene conversion / DNA replication initiation / DNA clamp unloading / Rad17 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic mismatch repair / epsilon DNA polymerase complex / Processive synthesis on the lagging strand / Elg1 RFC-like complex / Removal of the Flap Intermediate / Ctf18 RFC-like complex / telomere tethering at nuclear periphery / DNA replication factor C complex / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / SUMO binding / nucleotide-excision repair, DNA gap filling / Activation of the pre-replicative complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / PCNA complex / DNA replication proofreading / Translesion Synthesis by POLH / DNA replication checkpoint signaling / establishment of mitotic sister chromatid cohesion / single-stranded DNA 3'-5' DNA exonuclease activity / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / lagging strand elongation / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / sister chromatid cohesion / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / error-free translesion synthesis / leading strand elongation / DNA polymerase processivity factor activity / nuclear replication fork / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome, centromeric region / Dual incision in TC-NER / DNA replication initiation / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / error-prone translesion synthesis / base-excision repair, gap-filling / positive regulation of DNA repair / positive regulation of DNA replication / DNA damage checkpoint signaling / replication fork / nucleotide-excision repair / 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 / chromosome, telomeric region / DNA-directed DNA polymerase activity / DNA repair / mRNA binding / nucleotide binding / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / 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 ...Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / 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 / Replication factor C subunit 3, C-terminal domain / RCF1/5-like, AAA+ ATPase lid domain / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, delta subunit / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / 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 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribonuclease H superfamily / Ribonuclease H-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proliferating cell nuclear antigen / DNA polymerase epsilon catalytic subunit A / Sister chromatid cohesion protein DCC1 / Replication factor C subunit 5 / Replication factor C subunit 3 / Chromosome transmission fidelity protein 8 / Replication factor C subunit 4 / Replication factor C subunit 2 / Chromosome transmission fidelity protein 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYuan Z / Georgescu R / O'Donnell M / Li H
Funding support United States, 3 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)GM115809 United States
Howard Hughes Medical Institute (HHMI)M.E.O. United States
CitationJournal: 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
DepositionAug 20, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41664.png

Downloads & links

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Map

FileDownload / File: emd_41664.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.144
Minimum - Maximum-0.43016952 - 0.9632165
Average (Standard dev.)0.005474445 (±0.03695583)
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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Half map: #2

Fileemd_41664_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_41664_half_map_2.map
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Sample components

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Entire : Ctf18-RFC-PCNA-PolE-DNA complex

EntireName: Ctf18-RFC-PCNA-PolE-DNA complex
Components
  • Complex: Ctf18-RFC-PCNA-PolE-DNA complex
    • Protein or peptide: Chromosome transmission fidelity protein 18
    • DNA: Primer DNA
    • DNA: Template DNA
    • Protein or peptide: DNA polymerase epsilon catalytic subunit A
    • Protein or peptide: Chromosome transmission fidelity protein 8
    • Protein or peptide: Sister chromatid cohesion protein DCC1
    • Protein or peptide: Replication factor C subunit 4
    • Protein or peptide: Replication factor C subunit 3
    • Protein or peptide: Replication factor C subunit 2
    • Protein or peptide: Replication factor C subunit 5
    • Protein or peptide: Chromosome transmission fidelity protein 18
    • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Ctf18-RFC-PCNA-PolE-DNA complex

SupramoleculeName: Ctf18-RFC-PCNA-PolE-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Chromosome transmission fidelity protein 18

MacromoleculeName: Chromosome transmission fidelity protein 18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 3.171607 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
TVKIWVKYNE GFSNAVRKNV TWNNLW

UniProtKB: Chromosome transmission fidelity protein 18

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Macromolecule #4: DNA polymerase epsilon catalytic subunit A

MacromoleculeName: DNA polymerase epsilon catalytic subunit A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 255.992484 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

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Macromolecule #5: Chromosome transmission fidelity protein 8

MacromoleculeName: Chromosome transmission fidelity protein 8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 15.058493 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
PSVDIDASQW QKLTQSREKQ TTVITPLGMM MLEIQGELEL PKDFASLARR DSPNEGRFSE QDGETLIRFG SLQIDGERAT LFVGKKQRL LGKVTKLDVP MGIMHFNSKD NKVELVDVMK YKVIFKDRPL PIM

UniProtKB: Chromosome transmission fidelity protein 8

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Macromolecule #6: Sister chromatid cohesion protein DCC1

MacromoleculeName: Sister chromatid cohesion protein DCC1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 44.133785 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: 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

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Macromolecule #7: Replication factor C subunit 4

MacromoleculeName: Replication factor C subunit 4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 35.782516 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: TLSLQLPWVE KYRPQVLSDI VGNKETIDRL QQIAKDGNMP HMIISGMPGI GKTTSVHCLA HELLGRSYAD GVLELNASDD RGIDVVRNQ IKHFAQKKLH LPPGKHKIVI LDEADSMTAG AQQALRRTME LYSNSTRFAF ACNQSNKIIE PLQSRCAILR Y SKLSDEDV ...String:
TLSLQLPWVE KYRPQVLSDI VGNKETIDRL QQIAKDGNMP HMIISGMPGI GKTTSVHCLA HELLGRSYAD GVLELNASDD RGIDVVRNQ IKHFAQKKLH LPPGKHKIVI LDEADSMTAG AQQALRRTME LYSNSTRFAF ACNQSNKIIE PLQSRCAILR Y SKLSDEDV LKRLLQIIKL EDVKYTNDGL EAIIFTAEGD MRQAINNLQS TVAGHGLVNA DNVFKIVDSP HPLIVKKMLL AS NLEDSIQ ILRTDLWKKG YSSIDIVTTS FRVTKNLAQV KESVRLEMIK EIGLTHMRIL EGVGTYLQLA SMLAKIHKLN NK

UniProtKB: Replication factor C subunit 4

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Macromolecule #8: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.818879 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: SKENLPWVEK YRPETLDEVY GQNEVITTVR KFVDEGKLPH LLFYGPPGTG KTSTIVALAR EIYGKNYSNM VLELNASDDR GIDVVRNQI KDFASTRQIF SKGFKLIILD EADAMTNAAQ NALRRVIERY TKNTRFCVLA NYAHKLTPAL LSRCTRFRFQ P LPQEAIER ...String:
SKENLPWVEK YRPETLDEVY GQNEVITTVR KFVDEGKLPH LLFYGPPGTG KTSTIVALAR EIYGKNYSNM VLELNASDDR GIDVVRNQI KDFASTRQIF SKGFKLIILD EADAMTNAAQ NALRRVIERY TKNTRFCVLA NYAHKLTPAL LSRCTRFRFQ P LPQEAIER RIANVLVHEK LKLSPNAEKA LIELSNGDMR RVLNVLQSCK ATLDNPDEDE ISDDVIYECC GAPRPSDLKA VL KSILEDD WGTAHYTLNK VRSAKGLALI DLIEGIVKIL EDYELQNEET RVHLLTKLAD IEYSISKGGN DQIQGSAVIG AIK ASFENE T

UniProtKB: Replication factor C subunit 3

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Macromolecule #9: Replication factor C subunit 2

MacromoleculeName: Replication factor C subunit 2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.256617 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: SKLAAEQSLA QQPWVEKYRP KNLDEVTAQD HAVTVLKKTL KSANLPHMLF YGPPGTGKTS TILALTKELY GPDLMKSRIL ELNASDERG ISIVREKVKN FARLTVSKPS KHDLENYPCP PYKIIILDEA DSMTADAQSA LRRTMETYSG VTRFCLICNY V TRIIDPLA ...String:
SKLAAEQSLA QQPWVEKYRP KNLDEVTAQD HAVTVLKKTL KSANLPHMLF YGPPGTGKTS TILALTKELY GPDLMKSRIL ELNASDERG ISIVREKVKN FARLTVSKPS KHDLENYPCP PYKIIILDEA DSMTADAQSA LRRTMETYSG VTRFCLICNY V TRIIDPLA SRCSKFRFKA LDASNAIDRL RFISEQENVK CDDGVLERIL DISAGDLRRG ITLLQSASKG AQYLGDGKNI TS TQVEELA GVVPHDILIE IVEKVKSGDF DEIKKYVNTF MKSGWSAASV VNQLHEYYIT NDNFDTNFKN QISWLLFTTD SRL NNGTNE HIQLLNLLVK ISQL

UniProtKB: Replication factor C subunit 2

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Macromolecule #10: Replication factor C subunit 5

MacromoleculeName: Replication factor C subunit 5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.993582 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSLWVDKYRP KSLNALSHNE ELTNFLKSLS DQPRDLPHLL LYGPNGTGKK TRCMALLESI FGPGVYRLKI DVRQFVTASN RKLELNVVS SPYHLEITPS DMGNNDRIVI QELLKEVAQM EQVDFQDSKD GLAHRYKCVI INEANSLTKD AQAALRRTME K YSKNIRLI ...String:
MSLWVDKYRP KSLNALSHNE ELTNFLKSLS DQPRDLPHLL LYGPNGTGKK TRCMALLESI FGPGVYRLKI DVRQFVTASN RKLELNVVS SPYHLEITPS DMGNNDRIVI QELLKEVAQM EQVDFQDSKD GLAHRYKCVI INEANSLTKD AQAALRRTME K YSKNIRLI MVCDSMSPII APIKSRCLLI RCPAPSDSEI STILSDVVTN ERIQLETKDI LKRIAQASNG NLRVSLLMLE SM ALNNELA LKSSSPIIKP DWIIVIHKLT RKIVKERSVN SLIECRAVLY DLLAHCIPAN IILKELTFSL LDVETLNTTN KSS IIEYSS VFDERLSLGN KAIFHLEGFI AKVMCCLD

UniProtKB: Replication factor C subunit 5

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Macromolecule #11: Chromosome transmission fidelity protein 18

MacromoleculeName: Chromosome transmission fidelity protein 18 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.487195 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVDTAPYIGS LGRSSLFDTG DIEQAPGNNA IGINEEDIHA FVSSTGETVQ LKKKPAKLAT GNISLYTNPD TVWRSDDTYG ININYLLDK IEASGDDRTN AQKTSPITGK IGSDTLWVEK WRPKKFLDLV GNEKTNRRML GWLRQWTPAV FKEQLPKLPT E KEVSDMEL ...String:
MVDTAPYIGS LGRSSLFDTG DIEQAPGNNA IGINEEDIHA FVSSTGETVQ LKKKPAKLAT GNISLYTNPD TVWRSDDTYG ININYLLDK IEASGDDRTN AQKTSPITGK IGSDTLWVEK WRPKKFLDLV GNEKTNRRML GWLRQWTPAV FKEQLPKLPT E KEVSDMEL DPLKRPPKKI LLLHGPPGIG KTSVAHVIAK QSGFSVSEIN ASDERAGPMV KEKIYNLLFN HTFDTNPVCL VA DEIDGSI ESGFIRILVD IMQSDIKATN KLLYGQPDKK DKKRKKKRSK LLTRPIICIC NNLYAPSLEK LKPFCEIIAV KRP SDTTLL ERLNLICHKE NMNIPIKAIN DLIDLAQGDV RNCINNLQFL ASNVDSRDSS ASDKPACAKN TWASSNKDSP ISWF KIVNQ LFRKDPHRDI KEQFYELLNQ VELNGNSDRI LQGCFNIFPY VKYSDNGIRK PANISDWLFF HDLMYQSMYA HNGEL LRYS ALVPLVFFQT FGDIANKDDI RMKNSEYEQR ELKRANSDIV SLIMRHISVQ SPLMASFTDR KSLIFEILPY LDSMIS SDF NKIRNLKLKQ AIMEELVQLL KSFQLNLIQN RSEGFDVRGG LTIDPPIDEV VLLNPKHINE VQHKRANNLS SLLAKIE EN RAKKRHIDQV TEDRLQSQEM HSKKVKTGLN SSSSTIDFFK NQYGLLKQTQ ELEETQKTIG SDETNQADDC NQTVKIWV K YNEGFSNAVR KNVTWNNLWE

UniProtKB: Chromosome transmission fidelity protein 18

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Macromolecule #12: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.944051 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLEAKFEEAS LFKRIIDGFK DCVQLVNFQC KEDGIIAQAV DDSRVLLVSL EIGVEAFQEY RCDHPVTLGM DLTSLSKILR CGNNTDTLT LIADNTPDSI ILLFEDTKKD RIAEYSLKLM DIDADFLKIE ELQYDSTLSL PSSEFSKIVR DLSQLSDSIN I MITKETIK ...String:
MLEAKFEEAS LFKRIIDGFK DCVQLVNFQC KEDGIIAQAV DDSRVLLVSL EIGVEAFQEY RCDHPVTLGM DLTSLSKILR CGNNTDTLT LIADNTPDSI ILLFEDTKKD RIAEYSLKLM DIDADFLKIE ELQYDSTLSL PSSEFSKIVR DLSQLSDSIN I MITKETIK FVADGDIGSG SVIIKPFVDM EHPETSIKLE MDQPVDLTFG AKYLLDIIKG SSLSDRVGIR LSSEAPALFQ FD LKSGFLQ FFLAPKFNDE E

UniProtKB: Proliferating cell nuclear antigen

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Macromolecule #2: Primer DNA

MacromoleculeName: Primer DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.737795 KDa
SequenceString:
(DT)(DG)(DT)(DT)(DG)(DC)(DT)(DG)(DC)

+
Macromolecule #3: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.567998 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(DA)(DG) (DC)(DA)(DA)(DC)(DA)

+
Macromolecule #13: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #14: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 14 / Number of copies: 3 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #16: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87643
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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