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4fxd

Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA

Method: X-RAY DIFFRACTION Dmax: 149.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase alpha catalytic subunit A

Saccharomyces cerevisiae

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 Other combination Monomer Protein × 1 DNA 1 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 349–1258 Fragment：Polymerase domain, UNP residues 349-1258 ;DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3') ; × 1 ;RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3') ; × 1 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
2 Other combination Monomer Protein × 1 DNA 1 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain B； UniProt 349–1258 Fragment：Polymerase domain, UNP residues 349-1258 ;DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3') ; × 1 ;RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3') ; × 1 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

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 4FXD 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 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 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 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 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 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
4C93 Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha. Deposited 2013-10-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 137–149（13 aa） Fragment：CTF4-BINDING MOTIF, RESIDUES 137-149
Chain E 137–149（13 aa） Fragment：CTF4-BINDING MOTIF, RESIDUES 137-149
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 0.210
4FVM Crystal structure of yeast DNA polymerase alpha Deposited 2012-06-29 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
4FYD Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP Deposited 2012-07-04 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 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 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 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 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 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOA_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–910； UniProt 349–1258 Author chain B； PDBConstruct 1–910； UniProt 349–1258

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 4fxd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4fxd
Deposition date deposition_date2012-07-03
Structure title titleCrystal structure of yeast DNA polymerase alpha bound to DNA/RNA
Keywords keywordsDNA polymerase, DNA replication, TRANSFERASE-DNA-RNA complex; TRANSFERASE/DNA/RNA
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_guinier43.48 Å
Radius of gyration Rg (electron density) rg_electron43.29 Å
Forward intensity I(0) i0623648000.00
Molecular weight molecular_weight198990.0 kDa
Excluded volume excluded_volume246790 ų
Envelope volume envelope_volume345560 ų
Hydration-shell volume shell_volume67407 ų
Envelope diameter envelope_diameter149.4 Å
Shell Rg shell_rg47.14 Å
Envelope Rg envelope_rg42.86 Å
Shape Rg shape_rg43.29 Å
Total Rg total_rg43.49 Å
Total atoms total_atoms27701
Residues n_residues1687
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 dmax149.1 Å
Rg (real space) rg_real43.59 Å
Rg uncertainty (real space) rg_real_error1.40 Å
I(0) (real space) i0_real6.2360e+08
I(0) uncertainty (real space) i0_real_error1.1000e+07
Rg (reciprocal space) rg_reciprocal43.48 Å
I(0) (reciprocal space) i0_reciprocal623600000.0000
Solution quality estimate total_estimate0.8665
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.5 Å
Skewness Skewness skewness0.413
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha122900000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.878
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id4fxdA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily730 —
Domain ID domain_id4fxdA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2820 —
Domain ID domain_id4fxdA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id4fxdA04
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id4fxdA05
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id4fxdA06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily60 — B family DNA polymerase, thumb domain
Domain ID domain_id4fxdB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily730 —
Domain ID domain_id4fxdB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2820 —
Domain ID domain_id4fxdB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id4fxdB04
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology10 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily100 —
Domain ID domain_id4fxdB05
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id4fxdB06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily690 — B family DNA polymerase, finger domain
Domain ID domain_id4fxdB07
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily310 — B family DNA polymerase, thumb domain, four helix bundle
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8. Citations (1)

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9. Files and Curves (10)