SAXSdb — 4c93

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

DNA POLYMERASE ALPHA-BINDING PROTEIN

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 471–927 Chain B； UniProt 471–927 Chain C； UniProt 471–927	Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927	DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A × 2 （P13382）	X-RAY DIFFRACTION X-ray crystallization conditions：0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 2.69 Å R-free 0.210

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 4C93	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4C8H Crystal structure of the C-terminal region of yeast Ctf4, selenomethionine protein. Deposited 2013-10-01	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 471–927（457 aa） Fragment：C-TERMINAL DOMAIN Chain B 471–927（457 aa） Fragment：C-TERMINAL DOMAIN Chain C 471–927（457 aa） Fragment：C-TERMINAL DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 2.69 Å R-free 0.225
4C8S Crystal structure of the C-terminal region of yeast Ctf4 Deposited 2013-10-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain B 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain C 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 3.00 Å R-free 0.205
4C95 Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Sld5 Deposited 2013-10-02	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain B 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain C 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 2.69 Å R-free 0.214
5HOG Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2. Deposited 2016-01-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 450–927（478 aa） Fragment：UNP residues 450-927 Chain B 450–927（478 aa） Fragment：UNP residues 450-927 Chain C 450–927（478 aa） Fragment：UNP residues 450-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl.	Resolution 3.09 Å R-free 0.226
5HOI Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Tof2. Deposited 2016-01-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 472–927（456 aa） Fragment：UNP residues 472-927 Chain B 472–927（456 aa） Fragment：UNP residues 472-927 Chain C 472–927（456 aa） Fragment：UNP residues 472-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl	Resolution 3.30 Å R-free 0.224
5NXQ Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP Deposited 2017-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 471–927（457 aa） Fragment：UNP residues 471-927 Chain B 471–927（457 aa） Fragment：UNP residues 471-927 Chain C 471–927（457 aa） Fragment：UNP residues 471-927	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M tri-sodium citrate pH 6.2 7.5-9% (w/v) PEG 8000 0.40-0.65 M NaCI	Resolution 2.41 Å R-free 0.211
6PTJ Structure of Ctf4 trimer in complex with one CMG helicase Deposited 2019-07-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain E 1–927（927 aa） Chain F 1–927（927 aa） Chain G 1–927（927 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6PTN Structure of Ctf4 trimer in complex with two CMG helicases Deposited 2019-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain E 1–927（927 aa） Chain F 1–927（927 aa） Chain G 1–927（927 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
6PTO Structure of Ctf4 trimer in complex with three CMG helicases Deposited 2019-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain X 1–927（927 aa） Chain Y 1–927（927 aa） Chain Z 1–927（927 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6SKL Cryo-EM structure of the CMG Fork Protection Complex at a replication fork - Conformation 1 Deposited 2019-08-16	Different construct 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 F 1–927（927 aa） Fragment：Mcm6 Chain G 1–927（927 aa） Fragment：Mcm6 Chain H 1–927（927 aa） Fragment：Mcm6	Not recorded	ZN ZINC ION × 5 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Three microlitres of sample was applied on a grid and incubated for 15-30 s at 4 degC before manually blotting with filter paper for 10 s and plunge-freezing in liquid ethane.	Resolution 3.70 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain F 1–927（927 aa） Fragment：Mcm6 Chain G 1–927（927 aa） Fragment：Mcm6 Chain H 1–927（927 aa） Fragment：Mcm6	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
8B9A S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain H 1–927（927 aa） Chain K 1–927（927 aa） Chain L 1–927（927 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9B S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain H 1–927（927 aa） Chain K 1–927（927 aa） Chain L 1–927（927 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8KG6 Yeast replisome in state I Deposited 2023-08-17	Different construct 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 F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 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
8W7M Yeast replisome in state V Deposited 2023-08-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 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 construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 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 construct 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 F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 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

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTF4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–478； UniProt 471–927 Author chain B； PDBConstruct 22–478； UniProt 471–927 Author chain C； PDBConstruct 22–478； UniProt 471–927

DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A

OrganismNot specified

UniProt P13382

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain D； UniProt 137–149 Chain E； UniProt 137–149	Fragment：CTF4-BINDING MOTIF, RESIDUES 137-149	DNA POLYMERASE ALPHA-BINDING PROTEIN × 3 （Q01454）	X-RAY DIFFRACTION X-ray crystallization conditions：0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 2.69 Å R-free 0.210

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 4C93	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FLO Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit Deposited 2008-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1263–1468（206 aa） Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468	Not recorded	SO4 SULFATE ION × 19 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.218
3FLO Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit Deposited 2008-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1263–1468（206 aa） Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468	Not recorded	SO4 SULFATE ION × 15 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.218
3FLO Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit Deposited 2008-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1263–1468（206 aa） Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468	Not recorded	SO4 SULFATE ION × 16 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.218
3FLO Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit Deposited 2008-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1263–1468（206 aa） Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468	Not recorded	SO4 SULFATE ION × 15 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.218
3OIQ Crystal structure of yeast telomere protein Cdc13 OB1 and the catalytic subunit of DNA polymerase alpha Pol1 Deposited 2010-08-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 215–250（36 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；23% PEG3350, 0.2M Magnisium formate, 0.1M Tris-HCl, 5mM DTT, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.273
4B08 Yeast DNA polymerase alpha, Selenomethionine protein Deposited 2012-06-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 349–1258（910 aa） Fragment：POLYMERASE DOMAIN, RESIDUES 349-1258	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.4；0.1 M BICINE PH 8.0-9.4, 6-10% PEG 8000	Resolution 2.67 Å R-free 0.234
4FVM Crystal structure of yeast DNA polymerase alpha Deposited 2012-06-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 349–1258（910 aa） Fragment：Polymerase domain, UNP residues 349-1258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.4；291 K；0.1M Bicine, 6% PEG8000, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.236
4FXD Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA Deposited 2012-07-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain A 349–1258（910 aa） Fragment：Polymerase domain, UNP residues 349-1258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Bicine, 12% PEG3350, 10 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.285
4FXD Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA Deposited 2012-07-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain B 349–1258（910 aa） Fragment：Polymerase domain, UNP residues 349-1258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Bicine, 12% PEG3350, 10 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.285
4FYD Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP Deposited 2012-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 349–1258（910 aa） Fragment：Polymerase domain, UNP residues 349-1258	Mutation：R508A, N509A, D998N	DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；291 K；0.2M MgAc2, 10% PEG8000, microbatch, temperature 291K	Resolution 3.10 Å R-free 0.247
4FYD Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP Deposited 2012-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 349–1258（910 aa） Fragment：Polymerase domain, UNP residues 349-1258	Mutation：R508A, N509A, D998N	DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；291 K；0.2M MgAc2, 10% PEG8000, microbatch, temperature 291K	Resolution 3.10 Å R-free 0.247
8B9A S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	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 × 21 PDB declaration: 23-meric	Chain J 1–1468（1468 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9B S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	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 × 21 PDB declaration: 23-meric	Chain J 1–1468（1468 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9C S. cerevisiae pol alpha - replisome complex Deposited 2022-10-05	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: eicosameric	Chain J 1–1468（1468 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPOA_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–13； UniProt 137–149 Author chain E； PDBConstruct 1–13； UniProt 137–149

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4c93
Deposition date deposition_date	2013-10-02
Structure title title	Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha.
Keywords keywords	DNA REPLICATION, ADAPTOR PROTEIN, BETA PROPELLER DOMAIN; DNA REPLICATION
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	34.67 Å
Radius of gyration Rg (electron density) rg_electron	33.71 Å
Forward intensity I(0) i0	261228000.00
Molecular weight molecular_weight	133590.0 kDa
Excluded volume excluded_volume	168390 Å³
Envelope volume envelope_volume	216440 Å³
Hydration-shell volume shell_volume	51762 Å³
Envelope diameter envelope_diameter	112.2 Å
Shell Rg shell_rg	41.81 Å
Envelope Rg envelope_rg	33.72 Å
Shape Rg shape_rg	33.71 Å
Total Rg total_rg	34.32 Å
Total atoms total_atoms	9433
Residues n_residues	1171
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	109.3 Å
Rg (real space) rg_real	34.55 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	2.6120e+08
I(0) uncertainty (real space) i0_real_error	4.1630e+06
Rg (reciprocal space) rg_reciprocal	34.63 Å
I(0) (reciprocal space) i0_reciprocal	261200000.0000
Solution quality estimate total_estimate	0.9021
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.4 Å
Skewness Skewness skewness	0.184
Kurtosis Kurtosis kurtosis	-0.562
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	84620000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.916

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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 ALPHA-BINDING PROTEIN
Molecular weight formula_weight	54447.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9617

MGSSHHHHHHSQDPENLYFQGTGKFRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEGEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQLK

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	YEAST
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A
Molecular weight formula_weight	1513.6 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

IDNFDDILGEFES

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	160

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8. Citations (1)

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Unit-cell length a length_a	88.977 Å
Unit-cell length b length_b	99.998 Å
Unit-cell length c length_c	219.546 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.694 Å
Low-resolution limit resolution_low	49.205 Å
R factor r_factor	0.1737
R_work r_work	0.1718
R_free r_free	0.2099

fit	/app/data/saxs_computation/c9/4c93/4c93.fit
pddf	/app/data/pr_computation/c9/4c93/4c93.pr.out
profile	/app/data/saxs_computation/c9/4c93/4c93.dat

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha.

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

DNA POLYMERASE ALPHA-BINDING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

DNA POLYMERASE ALPHA 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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)