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- EMDB-42406: Cryo-EM map of the human CTF18-RFC alone in the apo state (State 1) -
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Open data
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Basic information
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Title | Cryo-EM map of the human CTF18-RFC alone in the apo state (State 1) | |||||||||
![]() | Primary sharpen EM map | |||||||||
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![]() | DNA clamp loader complex / ![]() | |||||||||
Function / homology | ![]() response to organophosphorus / Ctf18 RFC-like complex / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / DNA clamp loader activity / Polymerase switching on the C-strand of the telomere / single-stranded DNA helicase activity ...response to organophosphorus / Ctf18 RFC-like complex / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / DNA clamp loader activity / Polymerase switching on the C-strand of the telomere / single-stranded DNA helicase activity / DNA duplex unwinding / DNA strand elongation involved in DNA replication / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA synthesis involved in DNA repair / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / ATP-dependent activity, acting on DNA / Activation of ATR in response to replication stress / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wang F / He Q / Li H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC. Authors: Qing He / Feng Wang / Michael E O'Donnell / Huilin Li / ![]() Abstract: The DNA sliding clamp PCNA is a multipurpose platform for DNA polymerases and many other proteins involved in DNA metabolism. The topologically closed PCNA ring needs to be cracked open and loaded ...The DNA sliding clamp PCNA is a multipurpose platform for DNA polymerases and many other proteins involved in DNA metabolism. The topologically closed PCNA ring needs to be cracked open and loaded onto DNA by a clamp loader, e.g., the well-studied pentameric ATPase complex RFC (RFC1-5). The CTF18-RFC complex is an alternative clamp loader found recently to bind the leading strand DNA polymerase ε and load PCNA onto leading strand DNA, but its structure and the loading mechanism have been unknown. By cryo-EM analysis of in vitro assembled human CTF18-RFC-DNA-PCNA complex, we have captured seven loading intermediates, revealing a detailed PCNA loading mechanism onto a 3'-ss/dsDNA junction by CTF18-RFC. Interestingly, the alternative loader has evolved a highly mobile CTF18 AAA+ module likely to lower the loading activity, perhaps to avoid competition with the RFC and to limit its role to leading strand clamp loading. To compensate for the lost stability due to the mobile AAA+ module, CTF18 has evolved a unique β-hairpin motif that reaches across RFC2 to interact with RFC5, thereby stabilizing the pentameric complex. Further, we found that CTF18 also contains a separation pin to locally melt DNA from the 3'-end of the primer; this ensures its ability to load PCNA to any 3'-ss/dsDNA junction, facilitated by the binding energy of the E-plug to the major groove. Our study reveals unique structural features of the human CTF18-RFC and contributes to a broader understanding of PCNA loading by the alternative clamp loaders. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.9 KB 25.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 59.7 KB | ||
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() ![]() ![]() | 62.2 MB 111.1 MB 116.1 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8unjMC ![]() 8umtC ![]() 8umuC ![]() 8umvC ![]() 8umwC ![]() 8umyC ![]() 8un0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Primary sharpen EM map | ||||||||||||||||||||
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
-Additional map: Original unsharpen EM map
File | emd_42406_additional_1.map | ||||||||||||
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Annotation | Original unsharpen EM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Sharpen EM map by DeepEMhancer
File | emd_42406_additional_2.map | ||||||||||||
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Annotation | Sharpen EM map by DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map A
File | emd_42406_half_map_1.map | ||||||||||||
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Annotation | EM half map A | ||||||||||||
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Density Histograms |
-Half map: EM half map B
File | emd_42406_half_map_2.map | ||||||||||||
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Annotation | EM half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : the human clamp loader CTF18_RFC
Entire | Name: the human clamp loader CTF18_RFC |
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Components |
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-Supramolecule #1: the human clamp loader CTF18_RFC
Supramolecule | Name: the human clamp loader CTF18_RFC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Chromosome transmission fidelity protein 18 homolog
Macromolecule | Name: Chromosome transmission fidelity protein 18 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 107.523984 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: MEDYEQELCG VEDDFHNQFA AELEVLAELE GASTPSPSGV PLFTAGRPPR TFEEALARGD AASSPAPAAS VGSSQGGARK RQVDADLQP AGSLPHAPRI KRPRLQVVKR LNFRSEEMEE PPPPDSSPTD ITPPPSPEDL AELWGHGVSE AAADVGLTRA S PAARNPVL ...String: MEDYEQELCG VEDDFHNQFA AELEVLAELE GASTPSPSGV PLFTAGRPPR TFEEALARGD AASSPAPAAS VGSSQGGARK RQVDADLQP AGSLPHAPRI KRPRLQVVKR LNFRSEEMEE PPPPDSSPTD ITPPPSPEDL AELWGHGVSE AAADVGLTRA S PAARNPVL RRPPILEDYV HVTSTEGVRA YLVLRADPMA PGVQGSLLHV PWRGGGQLDL LGVSLASLKK QVDGERRERL LQ EAQKLSD TLHSLRSGEE EAAQPLGAPE EEPTDGQDAS SHCLWVDEFA PRHYTELLSD DFTNRCLLKW LKLWDLVVFG HER PSRKPR PSVEPARVSK EATAPGKWKS HEQVLEEMLE AGLDPSQRPK QKVALLCGPP GLGKTTLAHV IARHAGYSVV EMNA SDDRS PEVFRTRIEA ATQMESVLGA GGKPNCLVID EIDGAPVAAI NVLLSILNRK GPQEVGPQGP AVPSGGGRRR RAEGG LLMR PIICICNDQF APSLRQLKQQ AFLLHFPPTL PSRLVQRLQE VSLRQGMRAD PGVLAALCEK TDNDIRACIN TLQFLY SRG QRELSVRDVQ ATRVGLKDQR RGLFSVWQEV FQLPRAQRRR VGQDPALPAD TLLLGDGDAG SLTSASQRFY RVLHAAA SA GEHEKVVQGL FDNFLRLRLR DSSLGAVCVA LDWLAFDDLL AGAAHHSQSF QLLRYPPFLP VAFHVLFASS HTPRITFP S SQQEAQNRMS QMRNLIQTLV SGIAPATRSR ATPQALLLDA LCLLLDILAP KLRPVSTQLY STREKQQLAS LVGTMLAYS LTYRQERTPD GQYIYRLEPN VEELCRFPEL PARKPLTYQT KQLIAREIEV EKMRRAEASA RVENSPQVDG SPPGLEGLLG GIGEKGVHR PAPRNHEQRL EHIMRRAARE EQPEKDFFGR VVVRSTAVPS AGDTAPEQDS VERRMGTAVG RSEVWFRFNE G VSNAVRRS LYIRDLL UniProtKB: Chromosome transmission fidelity protein 18 homolog |
-Macromolecule #2: Replication factor C subunit 2
Macromolecule | Name: Replication factor C subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.203207 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA ...String: MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA LACNASDKII EPIQSRCAVL RYTKLTDAQI LTRLMNVIEK ERVPYTDDGL EAIIFTAQGD MRQALNNLQS TF SGFGFIN SENVFKVCDE PHPLLVKEMI QHCVNANIDE AYKILAHLWH LGYSPEDIIG NIFRVCKTFQ MAEYLKLEFI KEI GYTHMK IAEGVNSLLQ MAGLLARLCQ KTMAPVAS UniProtKB: ![]() |
-Macromolecule #3: Replication factor C subunit 5
Macromolecule | Name: Replication factor C subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.545512 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: METSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTSTI LACAKQLYKD KEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR RVIEKFTENT RFCLICNYLS K IIPALQSR ...String: METSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTSTI LACAKQLYKD KEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR RVIEKFTENT RFCLICNYLS K IIPALQSR CTRFRFGPLT PELMVPRLEH VVEEEKVDIS EDGMKALVTL SSGDMRRALN ILQSTNMAFG KVTEETVYTC TG HPLKSDI ANILDWMLNQ DFTTAYRNIT ELKTLKGLAL HDILTEIHLF VHRVDFPSSV RIHLLTKMAD IEYRLSVGTN EKI QLSSLI AAFQVTRDLI VAEA UniProtKB: ![]() |
-Macromolecule #4: Replication factor C subunit 4
Macromolecule | Name: Replication factor C subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.735711 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME ...String: MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME KESKTTRFCL ICNYVSRIIE PLTSRCSKFR FKPLSDKIQQ QRLLDIAKKE NVKISDEGIA YLVKVSEGDL RK AITFLQS ATRLTGGKEI TEKVITDIAG VIPAEKIDGV FAACQSGSFD KLEAVVKDLI DEGHAATQLV NQLHDVVVEN NLS DKQKSI ITEKLAEVDK CLADGADEHL QLISLCATVM QQLSQNC UniProtKB: ![]() |
-Macromolecule #5: Replication factor C subunit 3
Macromolecule | Name: Replication factor C subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 40.614332 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST ...String: MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST SKVIPPIRSR CLAVRVPAPS IEDICHVLST VCKKEGLNLP SQLAHRLAEK SCRNLRKALL MCEACRVQQY PF TADQEIP ETDWEVYLRE TANAIVSQQT PQRLLEVRGR LYELLTHCIP PEIIMKGLLS ELLHNCDGQL KGEVAQMAAY YEH RLQLGS KAIYHLEAFV AKFMALYKKF MEDGLEGMMF UniProtKB: ![]() |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 123 |
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Output model | ![]() PDB-8unj: |