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5v7m

PCNA mutant L126A/I128A Protein Defective in Gene Silencing

Method: X-RAY DIFFRACTION Dmax: 66.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proliferating cell nuclear antigen

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P15873

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–258 Mutation：L126A, I128A MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1M sodium cacodylate, pH 6.5, 0.2M magnesium chloride, 20% PEG 1000 Resolution 1.93 Å R-free 0.240
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–258 Mutation：L126A, I128A MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1M sodium cacodylate, pH 6.5, 0.2M magnesium chloride, 20% PEG 1000 Resolution 1.93 Å R-free 0.240

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 5V7M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1PLQ CRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY FACTOR PCNA Deposited 1995-01-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Not recorded HG MERCURY (II) ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1PLR CRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY FACTOR PCNA Deposited 1995-01-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1SXJ Crystal Structure of the Eukaryotic Clamp Loader (Replication Factor C, RFC) Bound to the DNA Sliding Clamp (Proliferating Cell Nuclear Antigen, PCNA) Deposited 2004-03-30 Different construct Different mutation/modification 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 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；292 K；PEG 3350, sodium chloride, CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.85 Å R-free 0.306
2OD8 Structure of a peptide derived from Cdc9 bound to PCNA Deposited 2006-12-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；1.6 M (NH4)2SO4, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.80 Å R-free 0.285
3F1W Crystal structure of a mutant proliferating cell nuclear antigen that blocks translesion synthesis Deposited 2008-10-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–258（258 aa）
Mutation：G178S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；2.06M ammonium sulfate, 0.1M Sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.255
3F1W Crystal structure of a mutant proliferating cell nuclear antigen that blocks translesion synthesis Deposited 2008-10-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：G178S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；2.06M ammonium sulfate, 0.1M Sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.255
3GPM Structure of the trimeric form of the E113G PCNA mutant protein Deposited 2009-03-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：E113G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；2.0 M ammonium sulfate and 0.1 M sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.80 Å R-free 0.312
3GPN Structure of the non-trimeric form of the E113G PCNA mutant protein Deposited 2009-03-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–258（258 aa）
Mutation：E113G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；1.6 M ammonium sulfate and 0.1 M sodium Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.273
3K4X Eukaryotic Sliding Clamp PCNA Bound to DNA Deposited 2009-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–257（257 aa）
Chain A 2–257（256 aa）
Chain A 2–258（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Na Acetate, 100 mM NaCl, 14% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.98 Å R-free 0.280
3L0W Structure of split monoubiquitinated PCNA with ubiquitin in position two Deposited 2009-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–163（163 aa） Fragment：N fragment
Chain B 165–255（91 aa） Fragment：ubi-C fragment
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04 M ammonium sulfate, 0.1 M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.314
3L0X Structure of split yeast PCNA Deposited 2009-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–163（163 aa） Fragment：N fragment
Chain B 165–258（94 aa） Fragment：C fragment
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1.9M ammonium sulfate, 0.1M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.267
3L10 Structure of split monoubiquitinated PCNA with ubiquitin in position one Deposited 2009-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–163（163 aa） Fragment：N fragment
Chain B 165–255（91 aa） Fragment：Ubi-C fragment
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04M ammonium sulfate, 0.1M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.314
3PGE Structure of sumoylated PCNA Deposited 2010-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 165–258（94 aa） Fragment：sumo-C fragment of PCNA
Chain B 1–163（163 aa） Fragment：N fragment of PCNA
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2.0M Ammonium Sulfate, 0.1M sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.253
3V60 Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–258（258 aa）
Mutation：K127G SO4 SULFATE ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；4% PEG 8000, 500 mM LiSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.249
3V61 Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–258（258 aa）
Mutation：K127G BA BARIUM ION × 13 NEQ N-ETHYLMALEIMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；21% MPD, 100 mM BaCl2, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.254
3V62 Structure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–258（258 aa）
Mutation：K127G NEQ N-ETHYLMALEIMIDE × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；1.9 M AMMONIUM SULFATE 4% PEG 400 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.90 Å R-free 0.237
3V62 Structure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–258（258 aa）
Mutation：K127G NEQ N-ETHYLMALEIMIDE × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；1.9 M AMMONIUM SULFATE 4% PEG 400 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.90 Å R-free 0.237
4L60 Structure of C81R Mutant PCNA Protein Defective in Mismatch Repair Deposited 2013-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–256（256 aa）
Mutation：C81R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；20% PEG3000, 0.2M NaCl, and HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Resolution 3.00 Å R-free 0.254
4L6P Structure of C22Y Mutant PCNA protein defective in DNA mismatch repair Deposited 2013-06-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–258（258 aa）
Mutation：C22Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2M AmSO4, 0.2M Lithium Sulfate Monohydrate, 0.1M Sodium Cacodylate Trihydrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.68 Å R-free 0.280
4L6P Structure of C22Y Mutant PCNA protein defective in DNA mismatch repair Deposited 2013-06-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–258（258 aa）
Mutation：C22Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2M AmSO4, 0.2M Lithium Sulfate Monohydrate, 0.1M Sodium Cacodylate Trihydrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.68 Å R-free 0.280
4L6P Structure of C22Y Mutant PCNA protein defective in DNA mismatch repair Deposited 2013-06-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–258（258 aa）
Mutation：C22Y GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2M AmSO4, 0.2M Lithium Sulfate Monohydrate, 0.1M Sodium Cacodylate Trihydrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.68 Å R-free 0.280
4YHR Crystal Structure of Yeast Proliferating Cell Nuclear Antigen Deposited 2015-02-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Protein solution: 15 mg/mL protein in 20 mM HEPES and 150 mM NaCL at pH 7.5. Crystallization solution: 2.2M ammonium sulfate, 0.2M ammonium fluoride. Hanging drop was 50% protein solution, 50% crystallization solution
Resolution 2.95 Å R-free 0.273
5JNE E2-SUMO-Siz1 E3-SUMO-PCNA complex Deposited 2016-04-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–258（258 aa）
Mutation：K77D, C81E, R110D, K127G, K164C ZN ZINC ION × 1 GOL GLYCEROL × 6 6LN ethane-1,2-dithiol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M Tris-HCl (pH 8.5), 5% PEG 10,000, 0.2 M NaCl, 10% glycerol, 3% dioxane
Resolution 2.85 Å R-free 0.250
5JNE E2-SUMO-Siz1 E3-SUMO-PCNA complex Deposited 2016-04-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 1–258（258 aa）
Mutation：K77D, C81E, R110D, K127G, K164C ZN ZINC ION × 1 GOL GLYCEROL × 4 6LN ethane-1,2-dithiol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M Tris-HCl (pH 8.5), 5% PEG 10,000, 0.2 M NaCl, 10% glycerol, 3% dioxane
Resolution 2.85 Å R-free 0.250
5T9D Structure of PCNA acetylated on K20 Deposited 2016-09-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–258（257 aa）
Chain B 2–258（257 aa）
Chain C 2–258（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1M NH4SO4, 0.1M citrate
Resolution 3.27 Å R-free 0.231
5V7K PCNA mutant D41A/D42A Protein Defective in Gene Silencing Deposited 2017-03-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：D41A, D42A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M sodium citrate, pH 5.43, 0.529 ammonium sulfate, 0.729M lithium sulfate
Resolution 3.05 Å R-free 0.227
5V7L PCNA mutant R61A/D63A Protein Defective in Gene Silencing Deposited 2017-03-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：R61A, D63A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M sodium citrate, pH 5.57, 0.671M ammonium sulfate, 0.994M lithium sulfate
Resolution 3.20 Å R-free 0.251
5ZUT Crystal Structure of Yeast PCNA in Complex with N24 Peptide Deposited 2018-05-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；n-Octyl-b-D-glu, NaCi pH 5.5, PEG 3350
Resolution 2.82 Å R-free 0.397
6CX2 S177G Mutant of Yeast PCNA Deposited 2018-04-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：S177G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；2.2M Ammonium sulfate 20% Glycerol
Resolution 3.10 Å R-free 0.244
6CX3 S179T Mutant of Yeast PCNA Deposited 2018-04-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：S179T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290.15 K；2.2M Ammonium sulfate 0.2 Sodium Formate
Resolution 3.10 Å R-free 0.269
6CX4 V180A Mutant of Yeast PCNA Deposited 2018-04-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：V180A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290.15 K；2.2M Ammonium Sulfate 0.2M Potassium Chloride 20% Glycerol
Resolution 3.08 Å R-free 0.267
6D0Q Structure of a DNA retention-prone PCNA variant Deposited 2018-04-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：D21K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；50 mM sodium citrate pH 5.6, 2 M (NH4)2SO4
Resolution 2.80 Å R-free 0.269
6D0R Structure of a DNA retention-prone PCNA variant Deposited 2018-04-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Mutation：D17K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；50 mM sodium citrate pH 5.3 and 1.7 M (NH4)2SO4
Resolution 2.86 Å R-free 0.276
6E49 Pif1 peptide bound to PCNA trimer Deposited 2018-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；298 K；100 mM MIB (Qiagen), pH 9.0, 25% PEG1500
Resolution 2.90 Å R-free 0.253
6W9W R80A PCNA mutant defective in BIR Deposited 2020-03-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–254（254 aa）
Mutation：R80A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2.2 M ammonium sulfate, 0.2 M ammonium formate
Resolution 2.65 Å R-free 0.243
6WAC FF248-249AA PCNA mutant defective in BIR Deposited 2020-03-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–253（253 aa）
Mutation：F248A, F249A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；magnesium chloride hexahydrate, sodium dimethylarsinic acid, PEG1000
Resolution 2.90 Å R-free 0.270
7TFH Atomic model of the S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to two DNA molecules, one at the 5'-recessed end and the other at the 3'-recessed end Deposited 2022-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
7TFI Atomic model of the S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to DNA with an open clamp Deposited 2022-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
7TFJ Atomic model of S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to DNA with a closed clamp ring Deposited 2022-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7THJ Structure of the yeast clamp loader (Replication Factor C RFC) bound to the sliding clamp (Proliferating Cell Nuclear Antigen PCNA) in an autoinhibited conformation Deposited 2022-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7THV Structure of the yeast clamp loader (Replication Factor C RFC) bound to the sliding clamp (Proliferating Cell Nuclear Antigen PCNA) in an autoinhibited conformation Deposited 2022-01-12 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 × 8 PDB declaration: octameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7TI8 Structure of the yeast clamp loader (Replication Factor C RFC) bound to the open sliding clamp (Proliferating Cell Nuclear Antigen PCNA) Deposited 2022-01-13 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 × 8 PDB declaration: octameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7TIB Structure of the yeast clamp loader (Replication Factor C RFC) bound to the open sliding clamp (Proliferating Cell Nuclear Antigen PCNA) and primer-template DNA Deposited 2022-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7TIC Structure of the yeast clamp loader (Replication Factor C RFC) bound to the sliding clamp (Proliferating Cell Nuclear Antigen PCNA) in an autoinhibited conformation Deposited 2022-01-13 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 × 8 PDB declaration: octameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7TID Structure of the yeast clamp loader (Replication Factor C RFC) bound to the sliding clamp (Proliferating Cell Nuclear Antigen PCNA) and primer-template DNA Deposited 2022-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7TKU Structure of the yeast clamp loader (Replication Factor C RFC) bound to the open sliding clamp (Proliferating Cell Nuclear Antigen PCNA) Deposited 2022-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7U19 RFC:PCNA bound to nicked DNA Deposited 2022-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7U1A RFC:PCNA bound to dsDNA with a ssDNA gap of six nucleotides Deposited 2022-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7U1P RFC:PCNA bound to DNA with a ssDNA gap of five nucleotides Deposited 2022-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8DQX Open state of RFC:PCNA bound to a 3' ss/dsDNA junction Deposited 2022-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
8DQZ Intermediate state of RFC:PCNA bound to a 3' ss/dsDNA junction Deposited 2022-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
8DR1 Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) Deposited 2022-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.14 Å
8DR3 Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD Deposited 2022-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8DR4 Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD Deposited 2022-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8DR6 Closed state of RFC:PCNA bound to a nicked dsDNA Deposited 2022-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.39 Å
8THW Cac1 PIP motif bound to PCNA Deposited 2023-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–258（258 aa）
Chain B 1–258（258 aa）
Chain C 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M magnesium acetate tetrahydrate (Mg Ac4H) and 11% w/v PEG3350
Resolution 2.60 Å R-free 0.267
8TW7 Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA complex in Apo state conformation I Deposited 2023-08-20 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 × 8 PDB declaration: octameric
Chain A 1–258（258 aa）
Chain B 1–258（258 aa）
Chain C 1–258（258 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TW8 Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA complex in Apo state conformation I Deposited 2023-08-20 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 × 8 PDB declaration: octameric
Chain A 1–258（258 aa）
Chain B 1–258（258 aa）
Chain C 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TWA Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex Deposited 2023-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain X 1–258（258 aa）
Chain Y 1–258（258 aa）
Chain Z 1–258（258 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8TWB Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-DNA complex Deposited 2023-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–258（258 aa）
Chain B 1–258（258 aa）
Chain C 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

55 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PCNA_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–265； UniProt 1–258

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 5v7m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5v7m
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5v7m
Deposition date deposition_date2017-03-20
Structure title titlePCNA mutant L126A/I128A Protein Defective in Gene Silencing
Keywords keywordsCAF-1, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.92 Å
Radius of gyration Rg (electron density) rg_electron19.74 Å
Forward intensity I(0) i013562000.00
Molecular weight molecular_weight28472.0 kDa
Excluded volume excluded_volume36005 ų
Envelope volume envelope_volume42735 ų
Hydration-shell volume shell_volume18503 ų
Envelope diameter envelope_diameter67.9 Å
Shell Rg shell_rg25.57 Å
Envelope Rg envelope_rg20.05 Å
Shape Rg shape_rg19.70 Å
Total Rg total_rg20.73 Å
Total atoms total_atoms4009
Residues n_residues255
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 dmax66.0 Å
Rg (real space) rg_real20.89 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real1.3560e+07
I(0) uncertainty (real space) i0_real_error1.6890e+05
Rg (reciprocal space) rg_reciprocal20.89 Å
I(0) (reciprocal space) i0_reciprocal13560000.0000
Solution quality estimate total_estimate0.8189
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9 Å
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.440
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1855000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5v7ma1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.2 — DNA polymerase processivity factor
Domain ID domain_idd5v7ma2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.2 — DNA polymerase processivity factor
Domain ID domain_idd5v7ma3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id5v7mA00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)