6qib

The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster

Method: X-RAY DIFFRACTION D_max: 100.7 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase epsilon catalytic subunit A

Saccharomyces cerevisiae

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 1–1187	Mutation：D290A, E292A	Primer_11ddC × 1 Template16 × 1 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

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 6QIB	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
6FWK The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide Deposited 2018-03-06	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）	Mutation：M644G	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
6FWK The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide Deposited 2018-03-06	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）	Mutation：M644G	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
6G0A The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution. Deposited 2018-03-16	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）	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 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 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：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 ligand/ion 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
6S1C P3221 crystal form of the Ctf18-1-8/Pol2(1-528) complex Deposited 2019-06-18	Different construct 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 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 construct 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 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	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 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	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 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	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 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）	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 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	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 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	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 41 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 6–1192； UniProt 1–1187

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6qib
Deposition date deposition_date	2019-01-18
Structure title title	The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster
Keywords keywords	Pol epsilon, DNA, complex, DNA BINDING PROTEIN, Fe-S, P-domain; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.29 Å
Radius of gyration Rg (electron density) rg_electron	32.56 Å
Forward intensity I(0) i0	291629000.00
Molecular weight molecular_weight	130860.0 kDa
Excluded volume excluded_volume	160800 Å³
Envelope volume envelope_volume	215750 Å³
Hydration-shell volume shell_volume	52909 Å³
Envelope diameter envelope_diameter	107.1 Å
Shell Rg shell_rg	41.20 Å
Envelope Rg envelope_rg	32.58 Å
Shape Rg shape_rg	32.60 Å
Total Rg total_rg	33.08 Å
Total atoms total_atoms	9176
Residues n_residues	1148
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.7 Å
Rg (real space) rg_real	33.03 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	2.9160e+08
I(0) uncertainty (real space) i0_real_error	4.2830e+06
Rg (reciprocal space) rg_reciprocal	33.15 Å
I(0) (reciprocal space) i0_reciprocal	291700000.0000
Solution quality estimate total_estimate	0.9015
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.0 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.507
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46190000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.905

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DNA polymerase epsilon catalytic subunit A
Molecular weight formula_weight	137202.7 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	D290A, E292A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9176

GGDPHMMFGKKKNNGGSSTARYSAGNKYNTLSNNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLTNMHATLVSQETLSSGSNGGGNSNDGERVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFEARKLLRPILQDNANNNVQRNIYNVAANGSEKVDAKHLIEDIREYDVPYHVRVSIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDSAVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDSIKAERDCASCDFNRPGKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIATK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Primer_11ddC
Molecular weight formula_weight	3293.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

TAACCGCGTTC

Entity 3 Entity 3 polymer

Description description	Template16
Molecular weight formula_weight	4889.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

CTCTTGAACGCGGTTA

Entity 4 Entity 4 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	158.360 Å
Unit-cell length b length_b	70.402 Å
Unit-cell length c length_c	154.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	78.480 Å
R factor r_factor	0.2265
R_work r_work	0.2234
R_free r_free	0.2856

fit	/app/data/saxs_computation/qi/6qib/6qib.fit
pddf	/app/data/pr_computation/qi/6qib/6qib.pr.out
profile	/app/data/saxs_computation/qi/6qib/6qib.dat

The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase epsilon catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)