Current Protein Identity：P09884
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1K0P NMR Structures of the Zinc Finger Domain of Human DNA Polymerase-alpha Deposited 2001-09-20 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 |
| 4Y97 Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2015-02-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1265–1444（180 aa）
Fragment：UNP residues 1265-1444
|
Not recorded | 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 |
| 4Y97 Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2015-02-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1265–1444（180 aa）
Fragment：UNP residues 1265-1444
|
Not recorded | 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 |
| 4Y97 Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2015-02-17 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1265–1444（180 aa）
Fragment：UNP residues 1265-1444
|
Not recorded | 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 |
| 4Y97 Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2015-02-17 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1265–1444（180 aa）
Fragment：UNP residues 1265-1444
|
Not recorded | 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 |
| 5EXR Crystal structure of human primosome Deposited 2015-11-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric（23） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric（8） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers |
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 |