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3flo

Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit

Method: X-RAY DIFFRACTION Dmax: 189.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase alpha subunit B

Saccharomyces cerevisiae

UniProt P38121

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 246–705 Fragment：UNP residues 246-705 DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 246–705 Fragment：UNP residues 246-705 DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） 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
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain E； UniProt 246–705 Fragment：UNP residues 246-705 DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain G； UniProt 246–705 Fragment：UNP residues 246-705 DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） 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

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 3FLO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 B 1–705（705 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 B 1–705（705 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 B 1–705（705 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOA2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–460； UniProt 246–705 Author chain C； PDBConstruct 1–460； UniProt 246–705 Author chain E； PDBConstruct 1–460； UniProt 246–705 Author chain G； PDBConstruct 1–460； UniProt 246–705

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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1263–1468 Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468 DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 1263–1468 Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468 DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 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
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain F； UniProt 1263–1468 Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468 DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain H； UniProt 1263–1468 Fragment：Cysteine-rich C-terminal domain, UNP residues 1263-1468 DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 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

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 3FLO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOA_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 1–206； UniProt 1263–1468 Author chain D； PDBConstruct 1–206； UniProt 1263–1468 Author chain F； PDBConstruct 1–206； UniProt 1263–1468 Author chain H； PDBConstruct 1–206； UniProt 1263–1468

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 3flo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3flo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3flo
Deposition date deposition_date2008-12-19
Structure title titleCrystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit
Keywords keywords;Protein-protein complex, phosphoesterase fold, OB fold, Zinc-binding motif, DNA replication, Nucleus, Phosphoprotein, DNA-binding, DNA-directed DNA polymerase, Nucleotidyltransferase, 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_guinier54.94 Å
Radius of gyration Rg (electron density) rg_electron55.11 Å
Forward intensity I(0) i01231590000.00
Molecular weight molecular_weight285640.0 kDa
Excluded volume excluded_volume354180 ų
Envelope volume envelope_volume528820 ų
Hydration-shell volume shell_volume82177 ų
Envelope diameter envelope_diameter185.6 Å
Shell Rg shell_rg54.98 Å
Envelope Rg envelope_rg54.07 Å
Shape Rg shape_rg55.07 Å
Total Rg total_rg55.23 Å
Total atoms total_atoms19981
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 dmax189.4 Å
Rg (real space) rg_real55.22 Å
Rg uncertainty (real space) rg_real_error2.20 Å
I(0) (real space) i0_real1.2320e+09
I(0) uncertainty (real space) i0_real_error2.5560e+07
Rg (reciprocal space) rg_reciprocal54.69 Å
I(0) (reciprocal space) i0_reciprocal1231000000.0000
Solution quality estimate total_estimate0.8316
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary58.8 Å
Skewness Skewness skewness0.452
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha67940000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.609
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3floA02
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3floB00
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_id3floC02
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3floD00
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_id3floE02
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3floF00
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_id3floG02
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3floH00
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)