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- EMDB-64201: Structure of CTF18-PCNA with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-64201
TitleStructure of CTF18-PCNA with ATP
Map dataSharpened map.
Sample
  • Complex: CTF18-PCNA
    • Protein or peptide: Chromosome transmission fidelity protein 18 homolog
    • Protein or peptide: Replication factor C subunit 2
    • Protein or peptide: Replication factor C subunit 5
    • Protein or peptide: Replication factor C subunit 4
    • Protein or peptide: Replication factor C subunit 3
    • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCTF18-RFC / human clamp loader / PCNA / sliding clamp / complex / ATP / DNA BINDING PROTEIN
Function / homology
Function and homology information


Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / DNA clamp loader activity / nuclear lamina ...Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / DNA clamp loader activity / nuclear lamina / Polymerase switching / positive regulation of DNA-directed DNA polymerase activity / Processive synthesis on the lagging strand / MutLalpha complex binding / PCNA complex / Telomere C-strand (Lagging Strand) Synthesis / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Polymerase switching on the C-strand of the telomere / replisome / Processive synthesis on the C-strand of the telomere / response to L-glutamate / Removal of the Flap Intermediate from the C-strand / HDR through Single Strand Annealing (SSA) / DNA strand elongation involved in DNA replication / response to dexamethasone / DNA synthesis involved in DNA repair / histone acetyltransferase binding / Impaired BRCA2 binding to RAD51 / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / ATP-dependent activity, acting on DNA / estrous cycle / Activation of ATR in response to replication stress / mismatch repair / translesion synthesis / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / nuclear estrogen receptor binding / replication fork / 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 / male germ cell nucleus / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / G2/M DNA damage checkpoint / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / DNA-templated DNA replication / cellular response to xenobiotic stimulus / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / DNA replication / chromosome, telomeric region / nuclear body / DNA repair / chromatin binding / centrosome / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
: / 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. ...: / 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 / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Replication factor C subunit 4 / Replication factor C subunit 2 / Replication factor C subunit 5 / Replication factor C subunit 3 / Chromosome transmission fidelity protein 18 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBriola GR / Tehseen M / Al-Amodi A / Nguyen PQ / Savva CG / Hamdan SM / De Biasio A
Funding support Saudi Arabia, 1 items
OrganizationGrant numberCountry
Other government Saudi Arabia
CitationJournal: To Be Published
Title: Structure of the human CTF18 clamp loader bound to PCNA with ATP
Authors: Briola G / Tehseen M / Al-Amodi A / Nguyen PQ / Savva CG / Hamdan SM / De Biasio A
History
DepositionApr 16, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64201.png

Downloads & links

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Map

FileDownload / File: emd_64201.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 220 pix.
= 204.6 Å		0.93 Å/pix.
x 220 pix.
= 204.6 Å		0.93 Å/pix.
x 220 pix.
= 204.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00611
Minimum - Maximum-0.009021559 - 0.021062361
Average (Standard dev.)0.00008388867 (±0.0010626644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 204.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64201_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_64201_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_64201_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CTF18-PCNA

EntireName: CTF18-PCNA
Components
  • Complex: CTF18-PCNA
    • Protein or peptide: Chromosome transmission fidelity protein 18 homolog
    • Protein or peptide: Replication factor C subunit 2
    • Protein or peptide: Replication factor C subunit 5
    • Protein or peptide: Replication factor C subunit 4
    • Protein or peptide: Replication factor C subunit 3
    • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: CTF18-PCNA

SupramoleculeName: CTF18-PCNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Details: CTF18 in complex with PCNA, in presence of ATP
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 323 KDa

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Macromolecule #1: Chromosome transmission fidelity protein 18 homolog

MacromoleculeName: Chromosome transmission fidelity protein 18 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.989062 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NPVLRRPPIL EDYVHVTSTE GVRAYLVLRA DPMAPGVQGS LLHVPWRGGG QLDLLGVSLA SLKKQVDGER RERLLQEAQK LSDTLHSLR SGEEEAAQPL GAPEEEPTDG QDASSHCLWV DEFAPRHYTE LLSDDFTNRC LLKWLKLWDL VVFGHERPSR K PRPSVEPA ...String:
NPVLRRPPIL EDYVHVTSTE GVRAYLVLRA DPMAPGVQGS LLHVPWRGGG QLDLLGVSLA SLKKQVDGER RERLLQEAQK LSDTLHSLR SGEEEAAQPL GAPEEEPTDG QDASSHCLWV DEFAPRHYTE LLSDDFTNRC LLKWLKLWDL VVFGHERPSR K PRPSVEPA RVSKEATAPG KWKSHEQVLE EMLEAGLDPS QRPKQKVALL CGPPGLGKTT LAHVIARHAG YSVVEMNASD DR SPEVFRT RIEAATQMES VLGAGGKPNC LVIDEIDGAP VAAINVLLSI LNRKGPQEVG PQGPAVPSGG GRRRRAEGGL LMR PIICIC NDQFAPSLRQ LKQQAFLLHF PPTLPSRLVQ RLQEVSLRQG MRADPGVLAA LCEKTDNDIR ACINTLQFLY SRGQ RELSV RDVQATRVGL KDQRRGLFSV WQEVFQLPRA QRRRVGQDPA LPADTLLLGD GDAGSLTSAS QRFYRVLHAA ASAGE HEKV VQGLFDNFLR LRLRDSSLGA VCVALDWLAF DDLLAGAAHH SQSFQLLRYP PFLPVAFHVL FASSHTPRIT FPSSQQ EAQ NRMSQMRNLI QTLVSGIAPA TRSRATPQAL LLDALCLLLD ILAPKLRPVS TQLYSTREKQ QLASLVGTML AYSLTYR QE RTPDGQYIYR LEPNVEELCR FPELPARKPL TYQTKQLIAR EIEVEKMRRA

UniProtKB: Chromosome transmission fidelity protein 18 homolog

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Macromolecule #2: Replication factor C subunit 2

MacromoleculeName: Replication factor C subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.621375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: YELPWVEKYR PVKLNEIVGN EDTVSRLEVF AREGNVPNII IAGPPGTGKT TSILCLARAL LGPALKDAML ELNASNDRGI DVVRNKIKM FAQQKVTLPK GRHKIIILDE ADSMTDGAQQ ALRRTMEIYS KTTRFALACN ASDKIIEPIQ SRCAVLRYTK L TDAQILTR ...String:
YELPWVEKYR PVKLNEIVGN EDTVSRLEVF AREGNVPNII IAGPPGTGKT TSILCLARAL LGPALKDAML ELNASNDRGI DVVRNKIKM FAQQKVTLPK GRHKIIILDE ADSMTDGAQQ ALRRTMEIYS KTTRFALACN ASDKIIEPIQ SRCAVLRYTK L TDAQILTR LMNVIEKERV PYTDDGLEAI IFTAQGDMRQ ALNNLQSTFS GFGFINSENV FKVCDEPHPL LVKEMIQHCV NA NIDEAYK ILAHLWHLGY SPEDIIGNIF RVCKTFQMAE YLKLEFIKEI GYTHMKIAEG VNSLLQMAGL LARLCQKTM

UniProtKB: Replication factor C subunit 2

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Macromolecule #3: Replication factor C subunit 5

MacromoleculeName: Replication factor C subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.330012 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NLPWVEKYRP QTLNDLISHQ DILSTIQKFI NEDRLPHLLL YGPPGTGKTS TILACAKQLY KDKEFGSMVL ELNASDDRGI DIIRGPILS FASTRTIFKK GFKLVILDEA DAMTQDAQNA LRRVIEKFTE NTRFCLICNY LSKIIPALQS RCTRFRFGPL T PELMVPRL ...String:
NLPWVEKYRP QTLNDLISHQ DILSTIQKFI NEDRLPHLLL YGPPGTGKTS TILACAKQLY KDKEFGSMVL ELNASDDRGI DIIRGPILS FASTRTIFKK GFKLVILDEA DAMTQDAQNA LRRVIEKFTE NTRFCLICNY LSKIIPALQS RCTRFRFGPL T PELMVPRL EHVVEEEKVD ISEDGMKALV TLSSGDMRRA LNILQSTNMA FGKVTEETVY TCTGHPLKSD IANILDWMLN QD FTTAYRN ITELKTLKGL ALHDILTEIH LFVHRVDFPS SVRIHLLTKM ADIEYRLSVG TNEKIQLSSL IAAFQVTRDL IVA

UniProtKB: Replication factor C subunit 5

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Macromolecule #4: Replication factor C subunit 4

MacromoleculeName: Replication factor C subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.769164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VPWVEKYRPK CVDEVAFQEE VVAVLKKSLE GADLPNLLFY GPPGTGKTST ILAAARELFG PELFRLRVLE LNASDERGIQ VVREKVKNF AQLTVSGSRS DGKPCPPFKI VILDEADSMT SAAQAALRRT MEKESKTTRF CLICNYVSRI IEPLTSRCSK F RFKPLSDK ...String:
VPWVEKYRPK CVDEVAFQEE VVAVLKKSLE GADLPNLLFY GPPGTGKTST ILAAARELFG PELFRLRVLE LNASDERGIQ VVREKVKNF AQLTVSGSRS DGKPCPPFKI VILDEADSMT SAAQAALRRT MEKESKTTRF CLICNYVSRI IEPLTSRCSK F RFKPLSDK IQQQRLLDIA KKENVKISDE GIAYLVKVSE GDLRKAITFL QSATRLTGGK EITEKVITDI AGVIPAEKID GV FAACQSG SFDKLEAVVK DLIDEGHAAT QLVNQLHDVV VENNLSDKQK SIITEKLAEV DKCLADGADE HLQLISLCAT VMQ QLSQ

UniProtKB: Replication factor C subunit 4

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Macromolecule #5: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.848395 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 MED

UniProtKB: Replication factor C subunit 3

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Macromolecule #6: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.393395 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

UniProtKB: Proliferating cell nuclear antigen

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / 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: 7.5 / Details: 50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 83.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 6181 / Average exposure time: 5.0 sec. / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1847264
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 602591
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6vvo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9uiq:
Structure of CTF18-PCNA with ATP

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