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4y97

Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit

Method: X-RAY DIFFRACTION Dmax: 152.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase alpha subunit B

Homo sapiens

UniProt Q14181

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 1–598 Not recorded DNA polymerase alpha catalytic subunit × 1 （P09884） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–598 Not recorded DNA polymerase alpha catalytic subunit × 1 （P09884） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 1–598 Not recorded DNA polymerase alpha catalytic subunit × 1 （P09884） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 1–598 Not recorded DNA polymerase alpha catalytic subunit × 1 （P09884） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257

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 4Y97 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KEB NMR solution structure of the N-terminal domain of the DNA polymerase alpha p68 subunit Deposited 2009-01-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–78（78 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 0.75 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
4E2I The Complex Structure of the SV40 Helicase Large T Antigen and p68 Subunit of DNA Polymerase Alpha-Primase Deposited 2012-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain 1 1–78（78 aa） Fragment：UNP residues 1-78
Chain 2 1–78（78 aa） Fragment：UNP residues 1-78
Chain 3 1–78（78 aa） Fragment：UNP residues 1-78
Chain 4 1–78（78 aa） Fragment：UNP residues 1-78
Chain 5 1–78（78 aa） Fragment：UNP residues 1-78
Chain 6 1–78（78 aa） Fragment：UNP residues 1-78
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.96 M sodium malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 5.00 Å R-free 0.314
4E2I The Complex Structure of the SV40 Helicase Large T Antigen and p68 Subunit of DNA Polymerase Alpha-Primase Deposited 2012-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain 7 1–78（78 aa） Fragment：UNP residues 1-78
Chain 8 1–78（78 aa） Fragment：UNP residues 1-78
Chain 9 1–78（78 aa） Fragment：UNP residues 1-78
Chain U 1–78（78 aa） Fragment：UNP residues 1-78
Chain W 1–78（78 aa） Fragment：UNP residues 1-78
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.96 M sodium malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 5.00 Å R-free 0.314
5EXR Crystal structure of human primosome Deposited 2015-11-24 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 D 2–598（597 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA
Resolution 3.60 Å R-free 0.326
5EXR Crystal structure of human primosome Deposited 2015-11-24 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 H 2–598（597 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA
Resolution 3.60 Å R-free 0.326
7OPL CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1 Deposited 2021-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 149–598（450 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
7U5C Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state Deposited 2022-03-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain D 1–598（598 aa）
Not recorded ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8B9D Human replisome bound by Pol Alpha Deposited 2022-10-05 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 A 1–598（598 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8D0B Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template Deposited 2022-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain G 143–598（456 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
8D0K Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template - PRIM2C advanced PIC Deposited 2022-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain G 2–598（597 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
8D9D Human DNA polymerase-alpha/primase elongation complex II bound to primer/template Deposited 2022-06-09 Different construct 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 D 155–598（444 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8QJ7 Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1 Deposited 2023-09-12 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 B 1–598（598 aa）
Not recorded ZN ZINC ION × 3 MN MANGANESE (II) ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VY3 Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio) Deposited 2024-02-06 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 D 155–598（444 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9C8V Human DNA polymerase alpha/primase - CHAPSO (4 mM) Deposited 2024-06-13 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 D 155–598（444 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å

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

View Construct and Data Evidence
UniProt name DPOA2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–598； UniProt 1–598 Author chain C； PDBConstruct 1–598； UniProt 1–598 Author chain E； PDBConstruct 1–598； UniProt 1–598 Author chain G； PDBConstruct 1–598； UniProt 1–598

DNA polymerase alpha catalytic subunit

Homo sapiens

UniProt P09884

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 1265–1444 Fragment：UNP residues 1265-1444 DNA polymerase alpha subunit B × 1 （Q14181） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 1265–1444 Fragment：UNP residues 1265-1444 DNA polymerase alpha subunit B × 1 （Q14181） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 1265–1444 Fragment：UNP residues 1265-1444 DNA polymerase alpha subunit B × 1 （Q14181） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 1265–1444 Fragment：UNP residues 1265-1444 DNA polymerase alpha subunit B × 1 （Q14181） ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl. Resolution 2.51 Å R-free 0.257

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 4Y97 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1K0P NMR Structures of the Zinc Finger Domain of Human DNA Polymerase-alpha Deposited 2001-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1347–1377（31 aa） Fragment：zinc finger domain (residues 1347-1377)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Pressure ambient
NMR sample composition 3mM Zinc Finger Domain; 3.6mM Zn(II)nitrate | 90% H2O/10% D2O
Resolution not provided
1K18 Minimized Average NMR Structure of the Zinc Finger Domain of Human DNA Polymerase-alpha Deposited 2001-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1347–1377（31 aa） Fragment：zinc finger domain (residues 1347-1377)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Pressure ambient
NMR sample composition 3mM Zinc Finger Peptide; 3.6 mM Zn(II)nitrate | 90% H2O/10% D2O
Resolution not provided
1N5G NMR Structures of the Zinc Finger Domain of Human DNA Polymerase-alpha Deposited 2002-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1345–1382（38 aa） Fragment：zinc finger domain (residues 1345-1382)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.2；296 K；Pressure ambient
NMR sample composition 3mM peptide, 3.6mM Zn(II)nitrate | 90% H2O/10% D2O
Resolution not provided
4BPX Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha Deposited 2013-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1445–1462（18 aa） Fragment：PRIMASE-BINDING MOTIF RESIDUES 1445-1462, PRIL RESIDUES 19-253
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL.
Resolution 3.40 Å R-free 0.267
4BPX Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha Deposited 2013-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1445–1462（18 aa） Fragment：PRIMASE-BINDING MOTIF RESIDUES 1445-1462, PRIL RESIDUES 19-253
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL.
Resolution 3.40 Å R-free 0.267
4Q5V Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and aphidicolin Deposited 2014-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric
Chain A 336–1257（922 aa） Fragment：Human DNA polymerase apha catalytic core domain residues 336-1257
Mutation：V516A 2ZE (3R,4R,4aR,6aS,8R,9R,11aS,11bS)-4,9-bis(hydroxymethyl)-4,11b-dimethyltetradecahydro-8,11a-methanocyclohepta[a]naphthale ne-3,9-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；100 mM KCl, 12.5 mM MgCl2, 25 mM Na-Cacodylate, pH 6.5, 6 % 2-propanol, 2 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 295 K
Resolution 2.52 Å R-free 0.268
4Q5V Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and aphidicolin Deposited 2014-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: trimeric
Chain E 336–1257（922 aa） Fragment：Human DNA polymerase apha catalytic core domain residues 336-1257
Mutation：V516A 2ZE (3R,4R,4aR,6aS,8R,9R,11aS,11bS)-4,9-bis(hydroxymethyl)-4,11b-dimethyltetradecahydro-8,11a-methanocyclohepta[a]naphthale ne-3,9-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；100 mM KCl, 12.5 mM MgCl2, 25 mM Na-Cacodylate, pH 6.5, 6 % 2-propanol, 2 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 295 K
Resolution 2.52 Å R-free 0.268
4QCL Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and dCTP Deposited 2014-05-12 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 336–1257（922 aa） Fragment：Human dna polymerase apha catalytic core domain residues 336-1257
Mutation：V516A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 3 K POTASSIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；reservoir solution: 0.8 mm zinc sulfate, 50 mm MES buffer pH 6.5, 8.8% v/v PEG MME 550; cryo solution: 100 mm potassium chloride, 0.8 mm zinc sulfate, 50 mm MES buffer pH 6.5, 1.1 magnesium chloride, 15% v/v PEG MME 550, 15% v/v ethylene glycol;, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.20 Å R-free 0.239
5EXR Crystal structure of human primosome Deposited 2015-11-24 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 C 335–1462（1128 aa）
Mutation：V516A ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA
Resolution 3.60 Å R-free 0.326
5EXR Crystal structure of human primosome Deposited 2015-11-24 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 G 335–1462（1128 aa）
Mutation：V516A ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA
Resolution 3.60 Å R-free 0.326
5IUD Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer Deposited 2016-03-17 Different construct 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 338–1255（918 aa） Fragment：UNP Residues 338-1255
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% polyethylene glycol 4000, 0.2M sodium citrate, 10% isopropanol, 0.1M sodium citrate buffer (pH = 5.5)
Resolution 3.30 Å R-free 0.228
5IUD Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer Deposited 2016-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 338–1255（918 aa） Fragment：UNP Residues 338-1255
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% polyethylene glycol 4000, 0.2M sodium citrate, 10% isopropanol, 0.1M sodium citrate buffer (pH = 5.5)
Resolution 3.30 Å R-free 0.228
5IUD Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer Deposited 2016-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain G 338–1255（918 aa） Fragment：UNP Residues 338-1255
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% polyethylene glycol 4000, 0.2M sodium citrate, 10% isopropanol, 0.1M sodium citrate buffer (pH = 5.5)
Resolution 3.30 Å R-free 0.228
5IUD Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer Deposited 2016-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain J 338–1255（918 aa） Fragment：UNP Residues 338-1255
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% polyethylene glycol 4000, 0.2M sodium citrate, 10% isopropanol, 0.1M sodium citrate buffer (pH = 5.5)
Resolution 3.30 Å R-free 0.228
6AS7 CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF HUMAN DNA POLYMERASE ALPHA IN TERNARY COMPLEX WITH AN DNA-PRIMED DNA TEMPLATE AND DCTP Deposited 2017-08-23 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 336–1257（922 aa）
Mutation：V516A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 CO COBALT (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；6MM COCL2, 2 MM TCEP, 50 MM NA ACETATE PH 4.6, 225 MM 1,6HEXADEDIOL
Resolution 2.95 Å R-free 0.301
7N2M Crystal structure of DNA polymerase alpha catalytic core in complex with dCTP and template/primer having T-C mismatch at the post-insertion site Deposited 2021-05-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric
Chain A 336–1257（922 aa）
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 4 K POTASSIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.8 mM zinc sulfate, 8.8% v/v PEG MME 550, and 50 mM MES pH 6.5
Resolution 2.90 Å R-free 0.228
7OPL CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1 Deposited 2021-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 334–1462（1129 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
7U5C Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state Deposited 2022-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain C 335–1462（1128 aa）
Not recorded ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8B9D Human replisome bound by Pol Alpha 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 B 1–1462（1462 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8D0B Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template Deposited 2022-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain F 324–1462（1139 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
8D0K Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template - PRIM2C advanced PIC Deposited 2022-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain F 2–1462（1461 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
8D96 Human DNA polymerase alpha/primase elongation complex I bound to primer/template Deposited 2022-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain C 1–1462（1462 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8D9D Human DNA polymerase-alpha/primase elongation complex II bound to primer/template Deposited 2022-06-09 Different construct 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 C 1–1462（1462 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8QJ7 Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1 Deposited 2023-09-12 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 1–1462（1462 aa）
Not recorded ZN ZINC ION × 3 MN MANGANESE (II) ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VY3 Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio) Deposited 2024-02-06 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 C 338–1456（1119 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9C8V Human DNA polymerase alpha/primase - CHAPSO (4 mM) Deposited 2024-06-13 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 C 338–1456（1119 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9MJ5 Catalytic domain of human DNA polymerase alpha in complex with DNA and RPA Deposited 2024-12-13 Different construct 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 S 335–1244（910 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

21 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOLA_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–180； UniProt 1265–1444 Author chain D； PDBConstruct 1–180； UniProt 1265–1444 Author chain F； PDBConstruct 1–180； UniProt 1265–1444 Author chain H； PDBConstruct 1–180； UniProt 1265–1444

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4y97

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4y97
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4y97
Deposition date deposition_date2015-02-17
Structure title titleCrystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit
Keywords keywordshuman DNA polymerase alpha, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.26 Å
Radius of gyration Rg (electron density) rg_electron48.66 Å
Forward intensity I(0) i01111020000.00
Molecular weight molecular_weight278210.0 kDa
Excluded volume excluded_volume348420 ų
Envelope volume envelope_volume501520 ų
Hydration-shell volume shell_volume85295 ų
Envelope diameter envelope_diameter149.9 Å
Shell Rg shell_rg53.99 Å
Envelope Rg envelope_rg46.93 Å
Shape Rg shape_rg48.65 Å
Total Rg total_rg48.91 Å
Total atoms total_atoms19522
Residues n_residues2464
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax152.1 Å
Rg (real space) rg_real49.01 Å
Rg uncertainty (real space) rg_real_error0.97 Å
I(0) (real space) i0_real1.1110e+09
I(0) uncertainty (real space) i0_real_error1.6990e+07
Rg (reciprocal space) rg_reciprocal49.26 Å
I(0) (reciprocal space) i0_reciprocal1111000000.0000
Solution quality estimate total_estimate0.8964
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.089
Kurtosis Kurtosis kurtosis-0.717
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha76290000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.744
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4y97B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily20 — DNA Polymerase alpha, zinc finger
Domain ID domain_id4y97D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily20 — DNA Polymerase alpha, zinc finger
Domain ID domain_id4y97F00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily20 — DNA Polymerase alpha, zinc finger
Domain ID domain_id4y97H00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily20 — DNA Polymerase alpha, zinc finger
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8. Citations (1)

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9. Files and Curves (10)