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6fwk

The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide

Method: X-RAY DIFFRACTION Dmax: 176.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase epsilon catalytic subunit A

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P21951

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 1–1186 Mutation：M644G ;DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3') ; × 1 ;DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3') ; × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 FE FE (III) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；50mM MES, 150mM NaAc and 8% PEG20K Resolution 2.50 Å R-free 0.263
2 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain B； UniProt 1–1186 Mutation：M644G ;DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3') ; × 1 ;DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3') ; × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 FE FE (III) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；50mM MES, 150mM NaAc and 8% PEG20K Resolution 2.50 Å R-free 0.263

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 6FWK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
28VY sCMGE assembled on ARS1 DNA with Sld2 and RPA Deposited 2026-02-23 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 × 13 PDB declaration: 15-meric
Chain G 1–2222（2222 aa）
Not recorded MG MAGNESIUM ION × 6 ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
4M8O TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP Deposited 2013-08-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1228（1228 aa） Fragment：POL2 domain, UNP residues 1-1228
Mutation：D290A,E292A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 TAU 2-AMINOETHANESULFONIC ACID × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine) , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.20 Å R-free 0.237
4PTF Ternary crystal structure of yeast DNA polymerase epsilon with template G Deposited 2014-03-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1187（1187 aa） Fragment：catalytic domain (UNP residues 1-1187)
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；12% PEG5000 MME, 25 mM magnesium acetate, 1% DMSO, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.81 Å R-free 0.247
5OKI Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon Deposited 2017-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–524（524 aa）
Mutation：D290A. E292A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 10000, 0.1 M MES pH 6.5, 0.2 M ammonium chloride
Resolution 4.50 Å R-free 0.312
5OKI Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon Deposited 2017-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–524（524 aa）
Mutation：D290A. E292A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 10000, 0.1 M MES pH 6.5, 0.2 M ammonium chloride
Resolution 4.50 Å R-free 0.312
6G0A The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution. Deposited 2018-03-16 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1186（1186 aa）
Mutation：P301R DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；50mM MES pH 6.5, 150mM NaAc and 8% PEG20K
Resolution 2.62 Å R-free 0.265
6H1V The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster Deposited 2018-07-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1187（1187 aa）
Mutation：D290A and E292A SF4 IRON/SULFUR CLUSTER × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine)
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine)
Resolution 2.70 Å R-free 0.266
6HV8 Cryo-EM structure of S. cerevisiae Polymerase epsilon deltacat mutant Deposited 2018-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1308–2221（914 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6I8A The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution. Deposited 2018-11-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1185（1185 aa）
Mutation：P301R DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；50mM MES pH 6.5, 150mM NaAc, 8%PEG20K
Resolution 2.65 Å R-free 0.279
6I8A The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution. Deposited 2018-11-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–1185（1185 aa）
Mutation：P301R DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；50mM MES pH 6.5, 150mM NaAc, 8%PEG20K
Resolution 2.65 Å R-free 0.279
6QIB The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster Deposited 2019-01-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1187（1187 aa）
Mutation：D290A, E292A SF4 IRON/SULFUR CLUSTER × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10mM Tris HCl pH8, 10mM CaCl2, 15% PEG8000
Resolution 2.80 Å R-free 0.286
6S1C P3221 crystal form of the Ctf18-1-8/Pol2(1-528) complex Deposited 2019-06-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–524（524 aa）
Mutation：D290A, E292A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 14% PEG 20000, 0.1 M HEPES pH 7.0
Resolution 6.10 Å R-free 0.333
6S1C P3221 crystal form of the Ctf18-1-8/Pol2(1-528) complex Deposited 2019-06-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–524（524 aa）
Mutation：D290A, E292A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 14% PEG 20000, 0.1 M HEPES pH 7.0
Resolution 6.10 Å R-free 0.333
6S2E Cryo-EM structure of Ctf18-1-8 in complex with the catalytic domain of DNA polymerase epsilon Deposited 2019-06-20 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 × 4 PDB declaration: tetrameric
Chain A 1–1186（1186 aa）
Mutation：D290A, E292A SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6S2F Cryo-EM structure of Ctf18-1-8 in complex with the catalytic domain of DNA polymerase epsilon (Class 2) Deposited 2019-06-20 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 × 4 PDB declaration: tetrameric
Chain A 1–1192（1192 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
6WJV Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme Deposited 2020-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2222（2222 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7PMK S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I) Deposited 2021-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–2222（2222 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger
Resolution 3.20 Å
7PMN S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II) Deposited 2021-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–2222（2222 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger
Resolution 3.20 Å
7QHS S. cerevisiae CMGE nucleating origin DNA melting Deposited 2021-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain G 1–2222（2222 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R3X The crystal structure of the L439V variant of Pol2CORE in complex with DNA and an incoming nucleotide Deposited 2022-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1185（1185 aa）
Mutation：L439V DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；8 % PEG 20K , 150 mM NaAc, 0-1,5% Glycerol, 50 mM MES pH6.5
Resolution 2.46 Å R-free 0.256
7Z13 S. cerevisiae CMGE dimer nucleating origin DNA melting Deposited 2022-02-24 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 × 26 PDB declaration: 28-meric
Chain N 1–2222（2222 aa）
Chain Q 1–2222（2222 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 8 ZN ZINC ION × 14 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8B67 The crystal structure of M644G variant of DNA Pol Epsilon containing CTP in the polymerase active site Deposited 2022-09-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：M644G CA CALCIUM ION × 3 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.60 Å R-free 0.276
8B6K The crystal structure of M644G variant of DNA Pol Epsilon containing dCTP in the polymerase active site Deposited 2022-09-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：M644G, D290A, E292A CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.50 Å R-free 0.260
8B6K The crystal structure of M644G variant of DNA Pol Epsilon containing dCTP in the polymerase active site Deposited 2022-09-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：M644G, D290A, E292A CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.50 Å R-free 0.260
8B76 The crystal structure of M644G variant of DNA Pol Epsilon containing dTTP in the polymerase active site Deposited 2022-09-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：M644G CA CALCIUM ION × 3 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.60 Å R-free 0.247
8B76 The crystal structure of M644G variant of DNA Pol Epsilon containing dTTP in the polymerase active site Deposited 2022-09-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：M644G CA CALCIUM ION × 3 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.60 Å R-free 0.247
8B77 The crystal structure of N828V variant of DNA Pol Epsilon containing dATP in the polymerase active site Deposited 2022-09-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1186（1186 aa）
Mutation：N828V DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.70 Å R-free 0.273
8B79 The crystal structure of M644G variant of DNA Pol Epsilon containing UTP in the polymerase active site Deposited 2022-09-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：M644G UTP URIDINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；50mM MES, PEG20K,2.5% glycerol, 150mM Sodium Actetate
Resolution 2.65 Å R-free 0.248
8B79 The crystal structure of M644G variant of DNA Pol Epsilon containing UTP in the polymerase active site Deposited 2022-09-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：M644G UTP URIDINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；50mM MES, PEG20K,2.5% glycerol, 150mM Sodium Actetate
Resolution 2.65 Å R-free 0.248
8B7E The crystal structure of N828V variant of DNA Pol Epsilon containing UTP in the polymerase active site Deposited 2022-09-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：N828V UTP URIDINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.60 Å R-free 0.230
8B7E The crystal structure of N828V variant of DNA Pol Epsilon containing UTP in the polymerase active site Deposited 2022-09-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–1186（1186 aa） Fragment：Catalytic subunit of DNA Pol Epsilon
Mutation：N828V UTP URIDINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；10mM Tris, 15% PEG8K,10mM CaCl2
Resolution 2.60 Å R-free 0.230
8KG6 Yeast replisome in state I Deposited 2023-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain M 1–2222（2222 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.
Resolution 3.07 Å
8KG8 Yeast replisome in state II Deposited 2023-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain M 1–2222（2222 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.
Resolution 4.23 Å
8KG9 Yeast replisome in state III Deposited 2023-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain M 1–2222（2222 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.
Resolution 4.52 Å
8P5E S. cerevisiae nexus-sCMGE after DNA replication initiation Deposited 2023-05-24 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 × 13 PDB declaration: 15-meric
Chain G 1–2222（2222 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8P62 S. cerevisiae ssDNA-sCMGE after DNA replication initiation Deposited 2023-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 14-meric
Chain G 1–2222（2222 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8P63 S. cerevisiae consensus-sCMGE on ssDNA after DNA replication initiation Deposited 2023-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 14-meric
Chain G 1–2222（2222 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 7 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TW9 Cryo-EM structure of S. cerevisiae PolE-Ctf18-8-1-DNA 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 × 4 PDB declaration: hexameric
Chain E 1–2222（2222 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 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 E 1–2222（2222 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
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15 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 × 27 PDB declaration: 29-meric
Chain 8 1–2222（2222 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

33 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOE_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–1191； UniProt 1–1186 Author chain B； PDBConstruct 6–1191； UniProt 1–1186

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 6fwk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6fwk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6fwk
Deposition date deposition_date2018-03-06
Structure title titleThe crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide
Keywords keywordsPol epsilon, M644G, DNA, complex, 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_guinier51.32 Å
Radius of gyration Rg (electron density) rg_electron51.92 Å
Forward intensity I(0) i01055540000.00
Molecular weight molecular_weight262310.0 kDa
Excluded volume excluded_volume324160 ų
Envelope volume envelope_volume476460 ų
Hydration-shell volume shell_volume77561 ų
Envelope diameter envelope_diameter182.7 Å
Shell Rg shell_rg53.33 Å
Envelope Rg envelope_rg51.34 Å
Shape Rg shape_rg51.98 Å
Total Rg total_rg51.78 Å
Total atoms total_atoms18418
Residues n_residues2252
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 dmax176.9 Å
Rg (real space) rg_real51.55 Å
Rg uncertainty (real space) rg_real_error1.76 Å
I(0) (real space) i0_real1.0560e+09
I(0) uncertainty (real space) i0_real_error1.9590e+07
Rg (reciprocal space) rg_reciprocal51.11 Å
I(0) (reciprocal space) i0_reciprocal1055000000.0000
Solution quality estimate total_estimate0.8331
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.6 Å
Skewness Skewness skewness0.450
Kurtosis Kurtosis kurtosis-0.515
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha115900000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.760
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)