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7qo1

complex of DNA ligase I and FEN1 on PCNA and DNA

Method: ELECTRON MICROSCOPY Dmax: 121.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA ligase 1

Homo sapiens

UniProt P18858

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 5 DNA 3 PDB declaration: octameric（8） Consistent with all polymer counts Chain A； UniProt 161–919 Not recorded Proliferating cell nuclear antigen × 3 （P12004） Oligo19ddC × 1 Oligo13P × 1 Oligo32 × 1 Flap endonuclease 1 × 1 （P39748） AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7QO1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1X9N Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA Deposited 2004-08-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 233–919（687 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；298 K；PEG 4000, sodium acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 3.00 Å R-free 0.268
6P09 Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+ Deposited 2019-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Not recorded MG MAGNESIUM ION × 5 PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；100 mM MES, 100 mM Lithium Acetate, 15% (w/v) polyethylene glycol 3350
Resolution 2.05 Å R-free 0.201
6P0A Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 2 mM Mg2+ Deposited 2019-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa） Fragment：residues 262-904
Not recorded MG MAGNESIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 100 mM Lithium Acetate, 15 % (w/v) PEG 3350
Resolution 2.05 Å R-free 0.203
6P0B Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+ Deposited 2019-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa） Fragment：residues 262-904
Mutation：E346A, E592A MG MAGNESIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 2.20 Å R-free 0.206
6P0C Human DNA Ligase 1 Bound to an Adenylated, hydroxyl terminated DNA nick in EDTA Deposited 2019-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa） Fragment：residues 262-904
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.55 Å R-free 0.165
6P0D Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, hydroxyl terminated DNA nick Deposited 2019-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Mutation：E346A, E592A PEG DI(HYDROXYETHYL)ETHER × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.75 Å R-free 0.179
6P0E Human DNA Ligase 1 (E346A,E592A) bound to adenylated DNA containing an 8-oxo guanine:adenine base-pair Deposited 2019-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa） Fragment：residues 262-904
Mutation：E346A, E592A PEG DI(HYDROXYETHYL)ETHER × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.184
6Q1V Human DNA Ligase 1 (E592R) Bound to an Adenylated, hydroxyl terminated DNA nick Deposited 2019-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Mutation：E592R PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350
Resolution 1.85 Å R-free 0.194
7KR3 Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate Deposited 2020-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Mutation：E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 150 mM lithium acetate, 10% (w/v) polyethylene glycol 3350
Resolution 2.78 Å R-free 0.239
7KR4 Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex Deposited 2020-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Mutation：E346A, E592A ACT ACETATE ION × 4 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 100 mM lithium acetate, 12% (w/v) polyethylene glycol 3350
Resolution 2.20 Å R-free 0.215
7L34 Human DNA Ligase 1 - R641L nicked DNA complex Deposited 2020-12-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–906（645 aa）
Mutation：R641L AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6, 100 mM lithium acetate, 15% (w/v) polyethylene glycol PEG3350
Resolution 1.90 Å R-free 0.193
7L35 Human DNA Ligase 1 - R771W nicked DNA complex Deposited 2020-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–906（645 aa）
Mutation：R771W PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6, 100 mM lithium acetate, 15% (w/v) polyethylene glycol PEG3350
Resolution 2.00 Å R-free 0.195
7QNZ human Lig1-DNA-PCNA complex reconstituted in absence of ATP Deposited 2021-12-23 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: heptameric
Chain A 1–919（919 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.58 Å
7SUM Crystal structure of human ligase I with nick duplexes containing cognate A:T Deposited 2021-11-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–918（658 aa） Fragment：UNP residues 261-918
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 6.6, 100 mM lithium acetate, 20% w/v PEG3350
Resolution 2.90 Å R-free 0.227
7SX5 Crystal structure of ligase I with nick duplexes containing mismatch A:C Deposited 2021-11-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–918（658 aa） Fragment：UNP residues 261-918
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；100 mM MES pH 6.6, 100 mM lithium acetate, 20% (w/v) polyethylene glycol PEG3350
Resolution 2.80 Å R-free 0.212
7SXE Crystal structure of ligase I with nick duplexes containing cognate G:T Deposited 2021-11-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–918（658 aa） Fragment：UNP residues 261-918
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 6.6, 100 mM lithium acetate, 20% w/v PEG3350
Resolution 3.00 Å R-free 0.245
8B8T Open conformation of the complex of DNA ligase I on PCNA and DNA in the presence of ATP Deposited 2022-10-05 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 262–535（274 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8V1U Human DNA Ligase I F872A bound to adenylated nicked DNA with a 5' terminal ribonucleotide Deposited 2023-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Mutation：F872A PEG DI(HYDROXYETHYL)ETHER × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；MES pH5.5 100mM, Lithium acetate 500mM, PEG 3350 10%
Resolution 2.00 Å R-free 0.210
8V1V Human DNA Ligase I F872L bound to adenylated nicked DNA Deposited 2023-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Mutation：F872L GOL GLYCEROL × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 AMP ADENOSINE MONOPHOSPHATE × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；MES pH5.5 100mM, Lithium acetate 500mM, PEG 3350 10%
Resolution 2.30 Å R-free 0.223
8V1W Human DNA Ligase I F872A bound to adenylated nicked DNA Deposited 2023-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–904（643 aa）
Mutation：F872A MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；MES pH5.5 100mM, Lithium acetate 500mM, PEG 3350 10%
Resolution 2.20 Å R-free 0.218
8VDN DNA Ligase 1 with nick dG:C Deposited 2023-12-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–918（658 aa） Fragment：UNP residues 261-918
Mutation：E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；100 mM MES, pH 6.4, 100 mM Lithium acetate, 12% w/v PEG 3350
Resolution 2.39 Å R-free 0.241
8VDS DNA Ligase 1 with nick DNA 3'rG:C Deposited 2023-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 261–918（658 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298.15 K；100 mM MES, pH 6.4, 100 mM Lithium acetate, 12% PEG3350
Resolution 2.79 Å R-free 0.252
8VDT DNA Ligase 1 with nick DNA 3'rA:T Deposited 2023-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 261–918（658 aa） Fragment：UNP residues 261-918
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298.5 K；100mM MES, pH 6.4, 100mM Lithium Acetate, 12 w/vPEG 3350
Resolution 2.78 Å R-free 0.249
8VZL DNA Ligase 1 captured with pre-step 3 ligation at the rG:C nicksite Deposited 2024-02-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–918（658 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.1 K；100 mM MES (pH 7.0), 100 mM lithium acetate, 14% (w/v) PEG3350
Resolution 2.41 Å R-free 0.219
8VZM DNA Ligase 1 captured with pre-step 3 ligation at the rA:T nicksite Deposited 2024-02-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–918（658 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298.1 K；100 mM MES (pH 6.7), 100 mM lithium acetate, 16% (w/v) PEG3350
Resolution 2.51 Å R-free 0.233
9BS3 Wild type DNA Ligase 1 with 5'-rG:C Deposited 2024-05-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–904（644 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298.15 K；100mM MES pH 5.3, 18% PEG3350, 100mM Lithium Acetate.
Resolution 2.69 Å R-free 0.249
9BS3 Wild type DNA Ligase 1 with 5'-rG:C Deposited 2024-05-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 261–904（644 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298.15 K；100mM MES pH 5.3, 18% PEG3350, 100mM Lithium Acetate.
Resolution 2.69 Å R-free 0.249
9BS4 DNA Ligase 1 E346A/E592A double mutant with 5'-rG:C Deposited 2024-05-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 261–904（644 aa）
Mutation：E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；298.5 K；100mM MES pH 5.3, 18% PEG3350, 100mM Lithium acetate
Resolution 2.40 Å R-free 0.237
9BS4 DNA Ligase 1 E346A/E592A double mutant with 5'-rG:C Deposited 2024-05-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 261–904（644 aa）
Mutation：E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；298.5 K；100mM MES pH 5.3, 18% PEG3350, 100mM Lithium acetate
Resolution 2.40 Å R-free 0.237
9NYS Human DNA Ligase 1 E346A/E592A/K845N triple mutant with 3'-A:T nick Deposited 2025-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–918（657 aa）
Mutation：E346A, E592A, K845N DMS DIMETHYL SULFOXIDE × 4 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100mM MES pH 7.0, 100 mM Litium Acetate, 20% (w/v) PEG 3350
Resolution 2.64 Å R-free 0.223
9YHU DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:A captured at post-catalytic stage Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 262–918（657 aa）
Mutation：E346A, E592A AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；100 mM MES (pH 6.5), 200 mM Lithium acetate, 12% (w/v) PEG3350
Resolution 1.96 Å R-free 0.203
9YHV DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:C captured at pre-catalytic stage Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–918（657 aa）
Mutation：E346A, E592A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；100 mM MES (pH 6.0), 150 mM Lithium acetate, 16% (w/v) PEG3350
Resolution 2.81 Å R-free 0.262
9YHW DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:A captured at pre-catalytic stage Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–918（657 aa）
Mutation：E346A, E592A DMS DIMETHYL SULFOXIDE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；100 mM MES (pH 6.5), 100 mM Lithium acetate, 12% (w/v) PEG3350
Resolution 2.56 Å R-free 0.229
9YHX DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:C captured at pre-catalytic stage Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–918（657 aa）
Mutation：E346A, E592A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；296 K；100 mM MES(pH 6.2), 200 mM Lithium acetate, 16% (w/v) PEG3350
Resolution 2.96 Å R-free 0.253
9YHY DNA ligase 1 wild-type in complex with nick containing 3'-8oxodG:C captured at pre-catalytic stage Deposited 2025-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 262–918（657 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；296 K；100 mM MES(pH 6.2), 200 mM Lithium acetate, 16% (w/v) PEG3350
Resolution 2.76 Å R-free 0.283

33 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNLI1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–760； UniProt 161–919

Proliferating cell nuclear antigen

Homo sapiens

UniProt P12004

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 5 DNA 3 PDB declaration: octameric（8） Consistent with all polymer counts Chain B； UniProt 1–261 Chain F； UniProt 1–261 Chain G； UniProt 1–261 Not recorded DNA ligase 1 × 1 （P18858） Oligo19ddC × 1 Oligo13P × 1 Oligo32 × 1 Flap endonuclease 1 × 1 （P39748） AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7QO1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AXC HUMAN PCNA Deposited 1997-10-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.289
1U76 Crystal structure of hPCNA bound to residues 452-466 of the DNA polymerase-delta-p66 subunit Deposited 2004-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.278
1U7B Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1) Deposited 2004-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.88 Å R-free 0.265
1UL1 Crystal structure of the human FEN1-PCNA complex Deposited 2003-09-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；6% PEG1000, 50mM MES, 50mM Sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.90 Å R-free 0.284
1VYJ Structural and biochemical studies of human PCNA complexes provide the basis for association with CDK/cyclin and rationale for inhibitor design Deposited 2004-04-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2.7M AS, HEPES PH8, pH 8.00
Resolution 2.80 Å R-free 0.256
1VYJ Structural and biochemical studies of human PCNA complexes provide the basis for association with CDK/cyclin and rationale for inhibitor design Deposited 2004-04-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–261（261 aa）
Chain I 1–261（261 aa）
Chain K 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2.7M AS, HEPES PH8, pH 8.00
Resolution 2.80 Å R-free 0.256
1VYM NATIVE HUMAN PCNA Deposited 2004-05-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20% PEG3350, 0.2M MAGNESIUM ACETATE, pH 7.00
Resolution 2.30 Å R-free 0.279
1W60 NATIVE HUMAN PCNA Deposited 2004-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；35% PEGMME 2K, 0.1M NA ACETATE (PH4.6), 0.2M AS., pH 4.60
Resolution 3.15 Å R-free 0.278
1W60 NATIVE HUMAN PCNA Deposited 2004-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；35% PEGMME 2K, 0.1M NA ACETATE (PH4.6), 0.2M AS., pH 4.60
Resolution 3.15 Å R-free 0.278
2ZVK Crystal structure of PCNA in complex with DNA polymerase eta fragment Deposited 2008-11-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.6；293 K；pH3.6, HANGING DROP VAPOR DIFFUSION, temperature 293K
Resolution 2.70 Å R-free 0.286
2ZVL Crystal structure of PCNA in complex with DNA polymerase kappa fragment Deposited 2008-11-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded SO4 SULFATE ION × 2 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION；pH 5.2；293 K；pH5.2, HANGING DROP VAPOR DIFFUSION, temperature 293K
Resolution 2.50 Å R-free 0.289
2ZVL Crystal structure of PCNA in complex with DNA polymerase kappa fragment Deposited 2008-11-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–261（261 aa）
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Not recorded SO4 SULFATE ION × 2 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION；pH 5.2；293 K；pH5.2, HANGING DROP VAPOR DIFFUSION, temperature 293K
Resolution 2.50 Å R-free 0.289
2ZVM Crystal structure of PCNA in complex with DNA polymerase iota fragment Deposited 2008-11-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION；pH 6.4；293 K；pH6.4, HANGING DROP VAPOR DIFFUSION, temperature 293K
Resolution 2.30 Å R-free 0.251
3JA9 Structure of native human PCNA Deposited 2015-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50mM Tris-HCl, 5mM MgCl2
Resolution 22.00 Å
3P87 Structure of human PCNA bound to RNASEH2B PIP box peptide Deposited 2010-10-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；293.15 K；3M NaCl, 0.1M citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.99 Å R-free 0.248
3P87 Structure of human PCNA bound to RNASEH2B PIP box peptide Deposited 2010-10-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain D 1–261（261 aa）
Chain F 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；293.15 K；3M NaCl, 0.1M citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.99 Å R-free 0.248
3P87 Structure of human PCNA bound to RNASEH2B PIP box peptide Deposited 2010-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；293.15 K；3M NaCl, 0.1M citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.99 Å R-free 0.248
3TBL Structure of Mono-ubiquitinated PCNA: Implications for DNA Polymerase Switching and Okazaki Fragment Maturation Deposited 2011-08-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.9 to 1.3 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.90 Å R-free 0.293
3VKX Structure of PCNA Deposited 2011-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Not recorded T3 3,5,3'TRIIODOTHYRONINE × 3 SO4 SULFATE ION × 18 CL CHLORIDE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.249
3WGW Structure of PCNA bound to a small molecule inhibitor Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Not recorded T2B 4-{4-[(2S)-2-amino-3-hydroxypropyl]-2,6-diiodophenoxy}phenol × 6 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.221
3WGW Structure of PCNA bound to a small molecule inhibitor Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–261（261 aa）
Not recorded T2B 4-{4-[(2S)-2-amino-3-hydroxypropyl]-2,6-diiodophenoxy}phenol × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.221
4D2G Crystal structure of human PCNA in complex with p15 peptide Deposited 2014-05-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 40% PEG 300 IN 0.1 MM PHOSPHATE-CITRATE PH 4.2
Resolution 2.65 Å R-free 0.250
4RJF Crystal structure of the human sliding clamp at 2.0 angstrom resolution Deposited 2014-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.08M strontium chloride hexahydrate, 0.02M magnesium chloride hexahydrate, 0.04M sodium cacodylate trihydrate (pH7.0), 20% v/v (+/-)-2-methyl-2,4-pentanediol and 0.012M spermine tetrahydrochloride, final [PCNA] = 11.6mg/mL = 0.40mM, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.01 Å R-free 0.189
4RJF Crystal structure of the human sliding clamp at 2.0 angstrom resolution Deposited 2014-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.08M strontium chloride hexahydrate, 0.02M magnesium chloride hexahydrate, 0.04M sodium cacodylate trihydrate (pH7.0), 20% v/v (+/-)-2-methyl-2,4-pentanediol and 0.012M spermine tetrahydrochloride, final [PCNA] = 11.6mg/mL = 0.40mM, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.01 Å R-free 0.189
4RJF Crystal structure of the human sliding clamp at 2.0 angstrom resolution Deposited 2014-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.08M strontium chloride hexahydrate, 0.02M magnesium chloride hexahydrate, 0.04M sodium cacodylate trihydrate (pH7.0), 20% v/v (+/-)-2-methyl-2,4-pentanediol and 0.012M spermine tetrahydrochloride, final [PCNA] = 11.6mg/mL = 0.40mM, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.01 Å R-free 0.189
4ZTD Crystal Structure of Human PCNA in complex with a TRAIP peptide Deposited 2015-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–254（253 aa） Fragment：UNP residues 2-254
Chain B 2–254（253 aa） Fragment：UNP residues 2-254
Chain C 2–254（253 aa） Fragment：UNP residues 2-254
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；16% PEG 6K in 0.1mM magnesium acetate, MES buffer pH 6.5
Resolution 2.20 Å R-free 0.234
5E0T Human PCNA mutant - S228I Deposited 2015-09-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Mutation：S228I Mutation：S228I Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100mM sodium acetate, pH4.5, 2M ammonium sulfate
Resolution 2.67 Å R-free 0.226
5E0T Human PCNA mutant - S228I Deposited 2015-09-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Mutation：S228I Mutation：S228I Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100mM sodium acetate, pH4.5, 2M ammonium sulfate
Resolution 2.67 Å R-free 0.226
5E0U Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms Deposited 2015-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–261（261 aa）
Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES pH 7.5, 25% PEG 3350
Resolution 1.93 Å R-free 0.221
5E0U Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms Deposited 2015-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–261（261 aa）
Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES pH 7.5, 25% PEG 3350
Resolution 1.93 Å R-free 0.221
5E0U Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms Deposited 2015-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–261（261 aa）
Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES pH 7.5, 25% PEG 3350
Resolution 1.93 Å R-free 0.221
5E0V Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms Deposited 2015-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–261（261 aa）
Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；2.35 M ammonium sulfate, 100 mM sodium acetate pH 4.6, 40% (v/v) -1,3-Butanediol
Resolution 2.07 Å R-free 0.229
5E0V Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms Deposited 2015-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–261（261 aa）
Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；2.35 M ammonium sulfate, 100 mM sodium acetate pH 4.6, 40% (v/v) -1,3-Butanediol
Resolution 2.07 Å R-free 0.229
5IY4 Crystal structure of human PCNA in complex with the PIP box of DVC1 Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；0.1 M Sodium citrate tribasic dehydrates (pH 5.0), 30% v/v Jeffamine ED-2001 (pH 7.0)
Resolution 2.94 Å R-free 0.270
5MAV Crystal structure of human PCNA in complex with PARG (poly(ADP-ribose) glycohydrolase) peptide. Deposited 2016-11-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；0.1 M Tris-HCl pH 7.5, 20% PEG 3350, 0.2 M ammonium acetate
Resolution 2.58 Å R-free 0.291
5MAV Crystal structure of human PCNA in complex with PARG (poly(ADP-ribose) glycohydrolase) peptide. Deposited 2016-11-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain D 1–261（261 aa）
Chain F 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；0.1 M Tris-HCl pH 7.5, 20% PEG 3350, 0.2 M ammonium acetate
Resolution 2.58 Å R-free 0.291
5MLO Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide Deposited 2016-12-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM NaCl + 8% (v/v) DMSO + 31% pentaerythitol propoxylate (5/4 PO/OH)
Resolution 1.96 Å R-free 0.259
5MLW Crystal structure of human PCNA in complex with ZRANB3 APIM motif peptide Deposited 2016-12-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100 mM lithium sulfate + 30% (w/v) polyvinylpyrrolidone + 100 mM HEPES pH 7.0
Resolution 2.45 Å R-free 0.264
5MOM Crystal Structure of PCNA encoding the hypomorphic mutation S228I Deposited 2016-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Chain B 1–258（258 aa）
Chain C 1–258（258 aa）
Mutation：S228I Mutation：S228I Mutation：S228I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.1M NaAcO, 2M (NH4)2SO4
Resolution 2.27 Å R-free 0.216
5YCO Complex structure of PCNA with UHRF2 Deposited 2017-09-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded GOL GLYCEROL × 3 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2 M ammonium sulfate, 0.1 M Tris pH 8.0
Resolution 2.20 Å R-free 0.220
5YCO Complex structure of PCNA with UHRF2 Deposited 2017-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–261（261 aa）
Not recorded GOL GLYCEROL × 3 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2 M ammonium sulfate, 0.1 M Tris pH 8.0
Resolution 2.20 Å R-free 0.220
5YD8 Crystal structure of human PCNA in complex with APIM of human ZRANB3 Deposited 2017-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350
Resolution 2.30 Å R-free 0.265
5YD8 Crystal structure of human PCNA in complex with APIM of human ZRANB3 Deposited 2017-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350
Resolution 2.30 Å R-free 0.265
5YD8 Crystal structure of human PCNA in complex with APIM of human ZRANB3 Deposited 2017-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350
Resolution 2.30 Å R-free 0.265
6CBI PCNA in complex with inhibitor Deposited 2018-02-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；2M ammonium sulfate 0.1M Tris pH8.0
Resolution 2.75 Å R-free 0.252
6CBI PCNA in complex with inhibitor Deposited 2018-02-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–261（261 aa）
Chain D 1–261（261 aa）
Chain F 1–261（261 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；2M ammonium sulfate 0.1M Tris pH8.0
Resolution 2.75 Å R-free 0.252
6EHT Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme Deposited 2017-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain A 1–254（254 aa）
Chain B 1–254（254 aa）
Chain C 1–255（255 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10% polyethylene glycol 3350 0.1 M sodium acetate pH 4.5
Resolution 3.20 Å R-free 0.327
6FCM Crystal structure of human PCNA Deposited 2017-12-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；19 to 23% PEG 3350, 0.2 to 0.3 M NaCl, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.276
6FCN Crystal structure of human PCNA soaked with p47phox(106-127) peptide Deposited 2017-12-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；19 to 23% PEG 3350, 0.2 to 0.3 M NaCl, 0.1 M Tris-HCl pH 8.5 12h prior to crystal freezing, 100 uM of p47phox(106-127) peptide was added to the crystallization drop
Resolution 3.22 Å R-free 0.272
6GIS Structural basis of human clamp sliding on DNA Deposited 2018-05-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Mutation：H from His tag Mutation：H from His tag Mutation：H from His tag No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；11% PEG 3350 0.1M Sodium acetate ph 4.5
Resolution 2.82 Å R-free 0.284
6GWS Crystal structure of human PCNA in complex with three p15 peptides Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；28% PEG 400, 0.2 M CaCl2, 0.1 M Hepes
Resolution 2.90 Å R-free 0.263
6HVO Crystal structure of human PCNA in complex with three peptides of p12 subunit of human polymerase delta Deposited 2018-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Bis Tris 6.5 , Li2SO4 (0.2M), PEG 3350 24%
Resolution 2.10 Å R-free 0.244
6K3A Crystal structure of human PCNA in complex with DNMT1 PIP box motif. Deposited 2019-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；1.6M sodium citrate
Resolution 2.30 Å R-free 0.264
6QC0 PCNA complex with Cdt2 C-terminal PIP-box peptide Deposited 2018-12-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10% (w/v) PEG 6000 100 mM MES/HCl
Resolution 3.50 Å R-free 0.252
6QCG PCNA complex with Cdt1 N-terminal PIP-box peptide Deposited 2018-12-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；300 K；15% (w/v) PEG 400, 100 mM calcium acetate, 100 mM MES/HCl
Resolution 3.40 Å R-free 0.253
6QCG PCNA complex with Cdt1 N-terminal PIP-box peptide Deposited 2018-12-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–261（261 aa）
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；300 K；15% (w/v) PEG 400, 100 mM calcium acetate, 100 mM MES/HCl
Resolution 3.40 Å R-free 0.253
6S1M Human polymerase delta holoenzyme Conformer 1 Deposited 2019-06-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Not recorded ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
6S1N Human polymerase delta holoenzyme Conformer 2 Deposited 2019-06-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Not recorded ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
6S1O Human polymerase delta holoenzyme Conformer 3 Deposited 2019-06-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Not recorded ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
6TNY Processive human polymerase delta holoenzyme Deposited 2019-12-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Not recorded ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
6TNZ Human polymerase delta-FEN1-PCNA toolbelt Deposited 2019-12-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Not recorded ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
6VVO Structure of the human clamp loader (Replication Factor C, RFC) bound to the sliding clamp (Proliferating Cell Nuclear Antigen, PCNA) Deposited 2020-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7EFA Crystal structure of the complex between the C-terminal domain of mouse MUTYH and human PCNA Deposited 2021-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG8000, imidazole
Resolution 2.70 Å R-free 0.286
7KQ0 PCNA bound to peptide mimetic Deposited 2020-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–259（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.18M magnesium acetate, 20% poly(ethylene) glycol 3350
Resolution 2.40 Å R-free 0.201
7KQ0 PCNA bound to peptide mimetic Deposited 2020-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–259（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.18M magnesium acetate, 20% poly(ethylene) glycol 3350
Resolution 2.40 Å R-free 0.201
7KQ0 PCNA bound to peptide mimetic Deposited 2020-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–259（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.18M magnesium acetate, 20% poly(ethylene) glycol 3350
Resolution 2.40 Å R-free 0.201
7KQ1 PCNA bound to truncated peptide mimetic Deposited 2020-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–259（259 aa）
Chain C 1–259（259 aa）
Chain E 1–259（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1M sodium malonate and 8% poly(ethylene)glycol 3350
Resolution 3.30 Å R-free 0.267
7M5L PCNA bound to peptide mimetic with linker Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–258（258 aa）
Chain B 1–258（258 aa）
Chain C 1–258（258 aa）
Not recorded TME PROPANE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.18M magnesium acetate, 19.2% poly(ethylene) glycol 3350
Resolution 3.00 Å R-free 0.275
7M5M PCNA bound to peptide mimetic Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–259（259 aa）
Chain B 1–259（259 aa）
Chain C 1–259（259 aa）
Not recorded NBU N-BUTANE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.18M Magnesium acetate, 19.5% poly(ethylene) glycol 3350
Resolution 3.00 Å R-free 0.274
7M5N PCNA bound to peptide mimetic with linker Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–259（259 aa）
Chain B 1–259（259 aa）
Chain C 1–259（259 aa）
Not recorded 8VH 1,3-dimethylbenzene × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.18M magnesium acetate, 19.3% poly(ethylene) glycol 3350
Resolution 3.11 Å R-free 0.309
7NV0 Human Pol Kappa holoenzyme with wt PCNA Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7NV1 Human Pol Kappa holoenzyme with Ub-PCNA Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7QNZ human Lig1-DNA-PCNA complex reconstituted in absence of ATP Deposited 2021-12-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: heptameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.58 Å
8B8T Open conformation of the complex of DNA ligase I on PCNA and DNA in the presence of ATP Deposited 2022-10-05 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–255（255 aa）
Chain F 1–255（255 aa）
Chain G 1–255（255 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8COB Crystal structure of human PCNA in complex with ERCC6L2 PIP box peptide Deposited 2023-02-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% (w/v) PEG3350, 100 mM BIS-TRIS pH 5.5
Resolution 2.73 Å R-free 0.255
8E84 Human PCNA mutant- C148S Deposited 2022-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–261（261 aa）
Mutation：C148S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；175 mM Magnesium Acetate, 20% PEG 3350
Resolution 3.10 Å R-free 0.292
8E84 Human PCNA mutant- C148S Deposited 2022-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–261（261 aa）
Mutation：C148S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；175 mM Magnesium Acetate, 20% PEG 3350
Resolution 3.10 Å R-free 0.292
8E84 Human PCNA mutant- C148S Deposited 2022-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–261（261 aa）
Mutation：C148S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；175 mM Magnesium Acetate, 20% PEG 3350
Resolution 3.10 Å R-free 0.292
8F5Q Crystal structure of human PCNA in complex with the PIP box of FBH1 Deposited 2022-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–259（259 aa）
Chain C 1–259（259 aa）
Chain E 1–259（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES, pH 7.5, 0.2 M magnesium chloride, 30% PEG400
Resolution 1.90 Å R-free 0.266
8GCJ PCNA Deposited 2023-03-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain C 1–261（261 aa）
Chain E 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.85 Å R-free 0.278
8GCJ PCNA Deposited 2023-03-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–261（261 aa）
Chain D 1–261（261 aa）
Chain F 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.85 Å R-free 0.278
8GL9 Co-crystal structure of caPCNA bound to AOH1160 derivative 1LE Deposited 2023-03-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded CL CHLORIDE ION × 6 ZQW N~2~-(naphthalene-1-carbonyl)-N-(2-phenoxyphenyl)-L-alpha-glutamine × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate, 0.2 M sodium chloride, 2.0 M ammonium sulfate
Resolution 2.81 Å R-free 0.240
8GL9 Co-crystal structure of caPCNA bound to AOH1160 derivative 1LE Deposited 2023-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 1–261（261 aa）
Not recorded CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate, 0.2 M sodium chloride, 2.0 M ammonium sulfate
Resolution 2.81 Å R-free 0.240
8GLA Co-crystal structure of caPCNA bound to the AOH1996 derivative, AOH1996-1LE Deposited 2023-03-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded ZQZ N-[2-(3-methoxyphenoxy)phenyl]-N~2~-(naphthalene-1-carbonyl)-L-alpha-glutamine × 6 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride, 2.0 M ammonium sulfate
Resolution 3.77 Å R-free 0.260
8GLA Co-crystal structure of caPCNA bound to the AOH1996 derivative, AOH1996-1LE Deposited 2023-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 1–261（261 aa）
Not recorded CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride, 2.0 M ammonium sulfate
Resolution 3.77 Å R-free 0.260
8UI7 Cryo-EM map of human clmap-clamp loader ATAD5-RFC-gapped PCNA complex in intermediate state 3 Deposited 2023-10-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 3 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8UI8 Cryo-EM map of human clamp-clamp loader ATAD5-RFC-two PCNAs complex in intermediate state 3 Deposited 2023-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 3 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UI9 Cryo-EM map of human clamp-clamp loader ATAD5-RFC-cracked PCNA complex in intermediate state 2 Deposited 2023-10-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8UII Cryo-EM map of human clamp-clamp loader ATAD5-RFC-closed PCNA complex in intermediate state 1 Deposited 2023-10-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8UMT Atomic model of the human CTF18-RFC-PCNA binary complex in the three-subunit binding state (state 2) Deposited 2023-10-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 3 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8UMU Atomic model of the human CTF18-RFC-PCNA binary complex in the four-subunit binding state (state 3) Deposited 2023-10-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 3 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
8UMV Atomic model of the human CTF18-RFC-PCNA-DNA ternary complex with narrow PCNA opening state I (state 5) Deposited 2023-10-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8UMW Atomic model of the human CTF18-RFC-PCNA-DNA ternary complex in the five-subunit binding state (state 4) Deposited 2023-10-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8UMY Atomic model of the human CTF18-RFC-PCNA-DNA ternary complex with narrow PCNA opening state II (state 6) Deposited 2023-10-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
8UN0 Atomic model of the human CTF18-RFC-PCNA-DNA ternary complex with cracked and closed PCNA (state 7) Deposited 2023-10-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8YJH Structure of the human endogenous PCNA-FEN1 complex - State A Deposited 2024-03-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
8YJL Structure of the human endogenous PCNA-FEN1 complex - State B Deposited 2024-03-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJQ Structure of the human endogenous PCNA-FEN1 complex - State C Deposited 2024-03-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJR Structure of the human endogenous PCNA-FEN1 complex - State D Deposited 2024-03-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJS Structure of the human endogenous PCNA-FEN1 complex - State E Deposited 2024-03-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8YJU Structure of the human endogenous PCNA-FEN1 complex - State F Deposited 2024-03-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
8YJV Structure of the human endogenous PCNA-FEN1 complex - State G Deposited 2024-03-03 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJW Structure of the human endogenous PCNA-FEN1 complex - State H Deposited 2024-03-03 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8YJZ Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D Deposited 2024-03-03 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: decameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
8ZWO Structure of CTF18-PCNA with ATP Deposited 2024-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
9B8S Human polymerase epsilon bound to PCNA and DNA in the nucleotide exchange state Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.01 Å
9B8T Human polymerase epsilon bound to PCNA and DNA in the nucleotide bound state Deposited 2024-03-31 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9CG4 Cryo-EM structure of FAN1, PCNA and DNA substrate with (CAG)2 extrusion in intermediate state Deposited 2024-06-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9CHM Cryo-EM structure of FAN1 R507H and PCNA in intermediate state Deposited 2024-07-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9CL7 Cryo-EM structure of FAN1-PCNA-DNA in final state Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
9CMA Cryo-EM structure of FAN1 R507H-PCNA-DNA in final state Deposited 2024-07-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
9EOA Cryo_EM structure of human FAN1 in complex with 5' flap DNA substrate and PCNA Deposited 2024-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: heptameric
Chain F 1–256（256 aa）
Chain G 1–256（256 aa）
Chain H 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
9F6D Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) Deposited 2024-05-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9F6E Human DNA polymerase epsilon bound to DNA and PCNA (ajar conformation) Deposited 2024-05-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.74 Å
9F6F Human DNA polymerase epsilon bound to DNA and PCNA (closed conformation) Deposited 2024-05-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9GY0 Cryo_EM structure of human FAN1 R507H mutant in complex with 5' flap DNA substrate and PCNA Deposited 2024-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: heptameric
Chain E 1–261（261 aa）
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Not recorded CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.42 Å
9IIN Structure of CTF18-PCNA with ATP and Mg2+ Deposited 2024-06-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–261（261 aa）
Chain G 1–261（261 aa）
Chain H 1–261（261 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9N3L Co-crystal structure of PCNA bound to HSP90alpha inhibitor, SNX2112 Deposited 2025-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–261（261 aa）
Not recorded E0G 4-[6,6-dimethyl-4-oxidanylidene-3-(trifluoromethyl)-5,7-dihydroindazol-1-yl]-2-[(4-oxidanylcyclohexyl)amino]benzamide × 3 CL CHLORIDE ION × 6 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium cacodylate pH 6.5, 0.2M sodium chloride, 2.0M ammonium sulfate
Resolution 1.90 Å R-free 0.233
9NE6 Human polymerase epsilon bound to PCNA and DNA with an in-situ-generated mismatch in the mismatch-editing state Deposited 2025-02-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
9NE7 Human polymerase epsilon bound to PCNA and DNA with an in-situ-generated mismatch in the Pol-backtracking state Deposited 2025-02-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
9NE8 Human polymerase epsilon bound to PCNA and DNA with an in-situ-generated mismatch in the mismatch-locking state Deposited 2025-02-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9NE9 Human polymerase epsilon bound to PCNA and DNA with a pre-existing mismatch in the blocked conformation I Deposited 2025-02-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.88 Å
9NEA Human polymerase epsilon bound to PCNA and DNA with a pre-existing mismatch in the blocked conformation II Deposited 2025-02-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.81 Å
9SRI Human DNA polymerase epsilon bound to DNA blunt end Deposited 2025-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Chain D 1–261（261 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9UIQ Structure of CTF18-PCNA with ATP Deposited 2025-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–257（257 aa）
Chain G 1–257（257 aa）
Chain H 1–257（257 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9VGW Crystal structure of human PCNA in complex with REV1 PIP-box Deposited 2025-06-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–261（261 aa）
Chain B 1–261（261 aa）
Chain C 1–261（261 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；ammonium sulfate
Resolution 2.70 Å R-free 0.261

101 other PDB entries and 126 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PCNA_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–264； UniProt 1–261 Author chain F； PDBConstruct 4–264； UniProt 1–261 Author chain G； PDBConstruct 4–264； UniProt 1–261

Flap endonuclease 1

Homo sapiens

UniProt P39748

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 5 DNA 3 PDB declaration: octameric（8） Consistent with all polymer counts Chain Y； UniProt 1–380 Mutation：D181A DNA ligase 1 × 1 （P18858） Proliferating cell nuclear antigen × 3 （P12004） Oligo19ddC × 1 Oligo13P × 1 Oligo32 × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7QO1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1U7B Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1) Deposited 2004-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 331–350（20 aa） Fragment：PIP-box region of FEN-1 (residues 331-350)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.88 Å R-free 0.265
1UL1 Crystal structure of the human FEN1-PCNA complex Deposited 2003-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain X 2–380（379 aa）
Chain Y 2–380（379 aa）
Chain Z 2–380（379 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；6% PEG1000, 50mM MES, 50mM Sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.90 Å R-free 0.284
3Q8K Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with product 5'-flap DNA, SM3+, and K+ Deposited 2011-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 2–336（335 aa）
Not recorded SM SAMARIUM (III) ION × 4 K POTASSIUM ION × 1 OH HYDROXIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；288 K；16% mPEG 2k, 20% saturated KCl, 0.5 mM Sm2(SO4)3, 10 mM Mg(NO3)2, 100 mM Hepes pH 7.0, 5% ethylene glycol, VAPOR DIFFUSION, temperature 288K
Resolution 2.20 Å R-free 0.213
3Q8L Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with substrate 5'-flap DNA, SM3+, and K+ Deposited 2011-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 2–336（335 aa）
Not recorded SM SAMARIUM (III) ION × 4 K POTASSIUM ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；288 K；17% mPEG 2k, 20% KCl, 0.5 mM Sm2(SO4)3, 50 mM Bis-Tris pH 7.0 and 5% Ethylene Glycol, vapor diffusion, temperature 288K
Resolution 2.32 Å R-free 0.202
3Q8M Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+ Deposited 2011-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 2–336（335 aa） Fragment：D181A
Not recorded K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；288 K；20% mPEG 2k, 20% KCl, 10 mM CaCl2, 50 mM Bis-Tris pH 7.5, 5% ethylene glycol, vapor diffusion, temperature 288K
Resolution 2.60 Å R-free 0.272
3Q8M Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+ Deposited 2011-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 2–336（335 aa） Fragment：D181A
Not recorded K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；288 K；20% mPEG 2k, 20% KCl, 10 mM CaCl2, 50 mM Bis-Tris pH 7.5, 5% ethylene glycol, vapor diffusion, temperature 288K
Resolution 2.60 Å R-free 0.272
3UVU Structural basis of nuclear import of Flap endonuclease 1 (FEN1) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 352–370（19 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；Sodium citrate, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.38 Å R-free 0.215
5FV7 Human Fen1 in complex with an N-hydroxyurea compound Deposited 2016-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–336（336 aa） Fragment：RESIDUES 1-336
Not recorded MG MAGNESIUM ION × 2 R3Z 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；25% PEG3350, 0.1M MOPS 7.0, 5% 2-PROPANOL, 2% GLYCEROL, pH 7.5
Resolution 2.84 Å R-free 0.300
5FV7 Human Fen1 in complex with an N-hydroxyurea compound Deposited 2016-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–336（336 aa） Fragment：RESIDUES 1-336
Not recorded MG MAGNESIUM ION × 2 R3Z 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；25% PEG3350, 0.1M MOPS 7.0, 5% 2-PROPANOL, 2% GLYCEROL, pH 7.5
Resolution 2.84 Å R-free 0.300
5K97 Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+ Deposited 2016-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain A 2–336（335 aa）
Mutation：D233N SM SAMARIUM (III) ION × 8 K POTASSIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；24% MPEG 2K, 20% KCl, 5% ethylene glycol, 100 mM HEPES pH 7.5
Resolution 2.10 Å R-free 0.219
5KSE Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA and Sm3+ Deposited 2016-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 2–336（335 aa）
Mutation：R100A SM SAMARIUM (III) ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；22% mPEG 2000, 20% saturated KCl, 5% ethylene glycol, 100 mM HEPES pH 7.5
Resolution 2.10 Å R-free 0.245
5UM9 Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+ Deposited 2017-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 2–336（335 aa）
Mutation：D86N K POTASSIUM ION × 1 SM SAMARIUM (III) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；6% MPEG 2K, 10% KCl, 50 mM HEPES pH 7.5, 2.5% Ethylene glycol, 1.06 mM SmSO4
Resolution 2.81 Å R-free 0.266
5ZOD Crystal Structure of hFen1 in apo form Deposited 2018-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–333（333 aa） Fragment：nuclease core
Not recorded MG MAGNESIUM ION × 2 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 1.90 Å R-free 0.226
5ZOE Crystal Structure of D181A hFen1 in complex with DNA Deposited 2018-04-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–333（333 aa） Fragment：nuclease core (1-333)
Mutation：D181A K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 1.95 Å R-free 0.227
5ZOF Crystal Structure of D181A/R192F hFen1 in complex with DNA Deposited 2018-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–333（333 aa） Fragment：nuclease core (1-333)
Mutation：D181A, R192F K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 2.25 Å R-free 0.269
5ZOG Crystal Structure of R192F hFen1 in complex with DNA Deposited 2018-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–333（333 aa） Fragment：nuclease core (1-333)
Mutation：R192F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 2.30 Å R-free 0.231
6TNZ Human polymerase delta-FEN1-PCNA toolbelt Deposited 2019-12-10 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain H 1–380（380 aa）
Not recorded ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
8YJH Structure of the human endogenous PCNA-FEN1 complex - State A Deposited 2024-03-01 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
8YJL Structure of the human endogenous PCNA-FEN1 complex - State B Deposited 2024-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJQ Structure of the human endogenous PCNA-FEN1 complex - State C Deposited 2024-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJR Structure of the human endogenous PCNA-FEN1 complex - State D Deposited 2024-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJS Structure of the human endogenous PCNA-FEN1 complex - State E Deposited 2024-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8YJU Structure of the human endogenous PCNA-FEN1 complex - State F Deposited 2024-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
8YJV Structure of the human endogenous PCNA-FEN1 complex - State G Deposited 2024-03-03 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJW Structure of the human endogenous PCNA-FEN1 complex - State H Deposited 2024-03-03 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8YJZ Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D Deposited 2024-03-03 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: decameric
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
9RCI Crystal Structure of Flap Endonuclease FEN1 with Compound 28 Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–336（336 aa）
Not recorded MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 A1JD4 (3~{S})-13-[(1~{S})-1-(2-methylquinolin-7-yl)ethoxy]-11-oxidanyl-5-oxa-1,8-diazatricyclo[8.4.0.0^{3,8}]tetradeca-10,13-diene-9,12-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 1.66 Å R-free 0.283
9RCI Crystal Structure of Flap Endonuclease FEN1 with Compound 28 Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–336（336 aa）
Not recorded MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 A1JD4 (3~{S})-13-[(1~{S})-1-(2-methylquinolin-7-yl)ethoxy]-11-oxidanyl-5-oxa-1,8-diazatricyclo[8.4.0.0^{3,8}]tetradeca-10,13-diene-9,12-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 1.66 Å R-free 0.283
9RDI Crystal Structure of Flap Endonuclease FEN1 with Compound 5 Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–336（336 aa）
Not recorded A1JED 2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione × 1 TEW 6-tungstotellurate(VI) × 4 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 2.10 Å R-free 0.232
9RDI Crystal Structure of Flap Endonuclease FEN1 with Compound 5 Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–336（336 aa）
Not recorded A1JED 2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione × 1 TEW 6-tungstotellurate(VI) × 5 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 2.10 Å R-free 0.232

26 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FEN1_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain Y； PDBConstruct 1–380； UniProt 1–380

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7qo1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7qo1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7qo1
Deposition date deposition_date2021-12-23
Structure title titlecomplex of DNA ligase I and FEN1 on PCNA and DNA
Keywords keywordsDNA, Replication, Complex, Ligase, PCNA, Ligation, FEN1, Flap Endonuclease I, Okazaki fragment maturation; REPLICATION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.32 Å
Radius of gyration Rg (electron density) rg_electron40.93 Å
Forward intensity I(0) i0696494000.00
Molecular weight molecular_weight203170.0 kDa
Excluded volume excluded_volume248800 ų
Envelope volume envelope_volume367000 ų
Hydration-shell volume shell_volume72540 ų
Envelope diameter envelope_diameter126.7 Å
Shell Rg shell_rg48.68 Å
Envelope Rg envelope_rg39.59 Å
Shape Rg shape_rg40.95 Å
Total Rg total_rg41.27 Å
Total atoms total_atoms14179
Residues n_residues1755
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax121.8 Å
Rg (real space) rg_real41.09 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real6.9650e+08
I(0) uncertainty (real space) i0_real_error1.1820e+07
Rg (reciprocal space) rg_reciprocal41.31 Å
I(0) (reciprocal space) i0_reciprocal696700000.0000
Solution quality estimate total_estimate0.8918
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.5 Å
Skewness Skewness skewness0.050
Kurtosis Kurtosis kurtosis-0.604
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85870000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.682
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)