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9f6f

Human DNA polymerase epsilon bound to DNA and PCNA (closed conformation)

Method: ELECTRON MICROSCOPY Dmax: 135.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase epsilon catalytic subunit A

Homo sapiens

UniProt Q07864

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 × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts Chain A； UniProt 1–1200 Mutation：D275A E277A Proliferating cell nuclear antigen × 3 （P12004） DNA nascent strand × 1 DNA template strand × 1 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

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 9F6F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5VBN Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2017-03-29 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 B 2142–2286（145 aa） Fragment：UNP residues 2142-2286
Not recorded SO4 SULFATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；50 mM sodium citrate, pH5.6, 0.70 M ammonium sulfate and 2 mM TCEP
Resolution 2.35 Å R-free 0.264
5VBN Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2017-03-29 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 F 2142–2286（145 aa） Fragment：UNP residues 2142-2286
Not recorded SO4 SULFATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；50 mM sodium citrate, pH5.6, 0.70 M ammonium sulfate and 2 mM TCEP
Resolution 2.35 Å R-free 0.264
7PFO Core human replisome Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain B 1–2286（2286 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7PLO H. sapiens replisome-CUL2/LRR1 complex Deposited 2021-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–2286（2286 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9B8S Human polymerase epsilon bound to PCNA and DNA in the nucleotide exchange state Deposited 2024-03-31 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–2286（2286 aa）
Mutation：D275A, E277A SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.01 Å
9F6D Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) Deposited 2024-05-01 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1200（1200 aa）
Mutation：D275A E277A 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1200（1200 aa）
Mutation：D275A E277A 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
9F6I Human DNA Polymerase epsilon bound to T-C mismatched DNA (Post-Insertion state) Deposited 2024-05-01 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1200（1200 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9F6J Human DNA Polymerase epsilon bound to T-C mismatched DNA (Polymerase Arrest state) Deposited 2024-05-01 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1200（1200 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9F6K Human DNA Polymerase epsilon bound to T-C mismatched DNA (Frayed Substrate state) Deposited 2024-05-01 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1200（1200 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9F6L Human DNA Polymerase epsilon bound to T-C mismatched DNA (Mismatch Excision state) Deposited 2024-05-01 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1200（1200 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
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 mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1200（1200 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 mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1200（1200 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 mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1200（1200 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 construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 27–1198（1172 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 construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–2286（2286 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1200（1200 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

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOE1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1200； UniProt 1–1200

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 × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts Chain B； UniProt 1–261 Chain C； UniProt 1–261 Chain D； UniProt 1–261 Not recorded DNA polymerase epsilon catalytic subunit A × 1 （Q07864） DNA nascent strand × 1 DNA template strand × 1 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

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 9F6F 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 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 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 ligand/ion 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
7QO1 complex of DNA ligase I and FEN1 on PCNA and DNA Deposited 2021-12-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: octameric
Chain B 1–261（261 aa）
Chain F 1–261（261 aa）
Chain G 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 4.40 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 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 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 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 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 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 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 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
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 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 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 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 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 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 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 1–261； UniProt 1–261 Author chain C； PDBConstruct 1–261； UniProt 1–261 Author chain D； PDBConstruct 1–261； UniProt 1–261

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 9f6f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9f6f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9f6f
Deposition date deposition_date2024-05-01
Structure title titleHuman DNA polymerase epsilon bound to DNA and PCNA (closed conformation)
Keywords keywordsDNA, polymerase, epsilon, PCNA, leading strand, human, replication, replisome, proofreading; 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_guinier43.44 Å
Radius of gyration Rg (electron density) rg_electron43.18 Å
Forward intensity I(0) i0887333000.00
Molecular weight molecular_weight234470.0 kDa
Excluded volume excluded_volume288870 ų
Envelope volume envelope_volume433690 ų
Hydration-shell volume shell_volume81562 ų
Envelope diameter envelope_diameter140.7 Å
Shell Rg shell_rg50.36 Å
Envelope Rg envelope_rg41.78 Å
Shape Rg shape_rg43.19 Å
Total Rg total_rg43.46 Å
Total atoms total_atoms16376
Residues n_residues1969
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 dmax135.8 Å
Rg (real space) rg_real43.26 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real8.8730e+08
I(0) uncertainty (real space) i0_real_error1.5910e+07
Rg (reciprocal space) rg_reciprocal43.44 Å
I(0) (reciprocal space) i0_reciprocal887500000.0000
Solution quality estimate total_estimate0.8943
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.8 Å
Skewness Skewness skewness0.181
Kurtosis Kurtosis kurtosis-0.517
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha136200000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.836
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)