Proliferating cell nuclear antigen
Homo sapiens
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 4 PDB declaration: octameric（8） Consistent with all polymer counts | Chain A； UniProt 1–261 Chain B； UniProt 1–261 Chain C； UniProt 1–261 | Not recorded | Flap endonuclease 1 × 1 （P39748） upstream DNA × 1 parent strand DNA × 1 5 prime flap DNA × 1 downstream DNA × 1 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 3.55 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 8YJW | 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 | Parsed fields agree | 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 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 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 |
| 8YJZ Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D Deposited 2024-03-03 | Different oligomeric state 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 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 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 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 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 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 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 | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–261； UniProt 1–261 Author chain B； PDBConstruct 1–261； UniProt 1–261 Author chain C； PDBConstruct 1–261； UniProt 1–261 |
