6hv8

Cryo-EM structure of S. cerevisiae Polymerase epsilon deltacat mutant

Method: ELECTRON MICROSCOPY D_max: 113.4 Å Quality: EXCELLENT

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

DNA polymerase epsilon subunit B

Saccharomyces cerevisiae

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–689	Not recorded	DNA polymerase epsilon catalytic subunit A × 1 （P21951） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6HV8	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 oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain F 1–689（689 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
6HV9 S. cerevisiae CMG-Pol epsilon-DNA Deposited 2018-10-10	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain B 1–689（689 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.98 Å
6WJV Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme Deposited 2020-04-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain 2 1–689（689 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain R 1–689（689 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain R 1–689（689 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain F 1–689（689 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
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 conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain F 1–689（689 aa） Chain M 1–689（689 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
8KG6 Yeast replisome in state I Deposited 2023-08-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric	Chain N 1–689（689 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain N 1–689（689 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain N 1–689（689 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 oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain F 1–689（689 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 oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 14-meric	Chain F 1–689（689 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 oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 14-meric	Chain F 1–689（689 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
8W7M Yeast replisome in state V Deposited 2023-08-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain N 1–689（689 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 5 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 4.12 Å
8W7S Yeast replisome in state IV Deposited 2023-08-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain N 1–689（689 aa）	Not recorded	No recorded non-water small molecule	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 7.39 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain 9 1–689（689 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
9RHI pre-Initiation Complex on ARS1 DNA (monomer) Deposited 2025-06-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric	Chain F 1–689（689 aa）	Not recorded	ZN ZINC ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9RHJ Pre-Initiation Complex on ARS1 DNA (dimer) Deposited 2025-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric	Chain F 1–689（689 aa） Chain M 1–689（689 aa）	Not recorded	ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPB2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–689； UniProt 1–689

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1308–2221	Not recorded	DNA polymerase epsilon subunit B × 1 （P24482） ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.40 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6HV8	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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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
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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 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 1–1186（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1192（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–2222（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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental method 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–914； UniProt 1308–2221

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	6hv8
Deposition date deposition_date	2018-10-10
Structure title title	Cryo-EM structure of S. cerevisiae Polymerase epsilon deltacat mutant
Keywords keywords	Polymerase epsilon, DNA replication, enzyme, DNA polymerase, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	36.72 Å
Radius of gyration Rg (electron density) rg_electron	35.69 Å
Forward intensity I(0) i0	253189000.00
Molecular weight molecular_weight	130790.0 kDa
Excluded volume excluded_volume	165020 Å³
Envelope volume envelope_volume	244880 Å³
Hydration-shell volume shell_volume	56504 Å³
Envelope diameter envelope_diameter	114.9 Å
Shell Rg shell_rg	42.77 Å
Envelope Rg envelope_rg	35.22 Å
Shape Rg shape_rg	35.69 Å
Total Rg total_rg	36.27 Å
Total atoms total_atoms	9206
Residues n_residues	1184
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	113.4 Å
Rg (real space) rg_real	36.53 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	2.5320e+08
I(0) uncertainty (real space) i0_real_error	3.6880e+06
Rg (reciprocal space) rg_reciprocal	36.65 Å
I(0) (reciprocal space) i0_reciprocal	253200000.0000
Solution quality estimate total_estimate	0.9078
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.5 Å
Skewness Skewness skewness	0.132
Kurtosis Kurtosis kurtosis	-0.597
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	64660000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA polymerase epsilon subunit B
Molecular weight formula_weight	78408.8 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	9206

MFGSGNVLPVKIQPPLLRPLAYRVLSRKYGLSIKSDGLSALAEFVGTNIGANWRQGPATIKFLEQFAAVWKQQERGLFIDQSGVKEVIQEMKEREKVEWSHEHPIQHEENILGRTDDDENNSDDEMPIAADSSLQNVSLSSPMRQPTERDEYKQPFKPESSKALDWRDYFKVINASQQQRFSYNPHKMQFIFVPNKKQNGLGGIAGFLPDIEDKVQMFLTRYYLTNDRVMRNENFQNSDMFNPLSSMVSLQNELSNTNRQQQSSSNSITPIKNLLGRDAQNFLLLGLLNKNFKGNWSLEDPSGSVEIDISQTIPTQGHYYVPGCMVLVEGIYYSVGNKFHVTSMTLPPGERREITLETIGNLDLLGIHGISNNNFIARLDKDLKIRLHLLEKELTDHKFVILGANLFLDDLKIMTALSKILQKLNDDPPTLLIWQGSFTSVPVFASMSSRNISSSTQFKNNFDALATLLSRFDNLTENTTMIFIPGPNDLWGSMVSLGASGTLPQDPIPSAFTKKINKVCKNVVWSSNPTRIAYLSQEIVIFRDDLSGRFKRHRLEFPFNESEDVYTENDNMMSKDTDIVPIDELVKEPDQLPQKVQETRKLVKTILDQGHLSPFLDSLRPISWDLDHTLTLCPIPSTMVLCDTTSAQFDLTYNGCKVINPGSFIHNRRARYMEYVPSSKKTIQEEIYI

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	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	DNA polymerase epsilon catalytic subunit A
Molecular weight formula_weight	104984.8 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

SMIRKQAESYANSTWEVLQYKDSGEPGVLEVFVTINGKVQNITFHIPKTIYMKFKSQTMPLQKIKNCLIEKSSASLPNNPKTSNPAGGQLFKITLPESVFLEEKENCTSIFNDENVLGVFEGTITPHQRAIMDLGASVTFRSKAMGALGKGIQQGFEMKDLSMAENERYLSGFSMDIGYLLHFPTSIGYEFFSLFKSWGDTITILVLKPSNQAQEINASSLGQIYKQMFEKKKGKIETYSYLVDIKEDINFEFVYFTDISKLYRRLSQETTKLKEERGLQFLLLLQSPFITKLLGTIRLLNQMPIVKLSLNEVLLPQLNWQPTLLKKLVNHVLSSGSWISHLIKLSQYSNIPICNLRLDSMDYIIDVLYARKLKKENIVLWWNEKAPLPDHGGIQNDFDLNTSWIMNDSEFPKINNSGVYDNVVLDVGVDNLTVNTILTSALINDAEGSDLVNNNMGIDDKDAVINSPSEFVHDAFSNDALNVLRGMLKEWWDEALKENSTADLLVNSLASWVQNPNAKLFDGLLRYHVHNLTKKALLQLVNEFSALGSTIVYADRNQILIKTNKYSPENCYAYSQYMMKAVRTNPMFSYLDLNIKRYWDLLIWMDKFNFSGLACIEIEEKENQDYTAVSQWQLKKFLSPIYQPEFEDWMMIILDSMLKTKQSYLKLNSGTQRPTQIVNVKKQDKEDSVENSLNGFSHLFSKPLMKRVKKLFKNQQEFILDPQYEADYVIPVLPGSHLNVKNPLLELVKSLCHVMLLSKSTILEIRTLRKELLKIFELREFAKVAEFKDPSLSLVVPDFLCEYCFFISDIDFCKAAPESIFSCVRCHKAFNQVLLQEHLIQKLRSDIESYLIQDLRCSRCHKVKRDYMSAHCPCAGAWEGTLPRESIVQKLNVFKQVAKYYGFDILLSCIADLT

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	Saccharomyces cerevisiae

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Resolution resolution	4.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	161376

fit	/app/data/saxs_computation/hv/6hv8/6hv8.fit
pddf	/app/data/pr_computation/hv/6hv8/6hv8.pr.out
profile	/app/data/saxs_computation/hv/6hv8/6hv8.dat

Cryo-EM structure of S. cerevisiae Polymerase epsilon deltacat mutant

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

DNA polymerase epsilon subunit B

State in the Current Structure

Other States of the Same Protein in the Database

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)