SAXSdb — 3flo

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

DNA polymerase alpha subunit B

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） SULFATE ION × 19 ZINC ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） SULFATE ION × 15 ZINC ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） SULFATE ION × 16 ZINC ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha catalytic subunit A × 1 DNA polymerase alpha catalytic subunit A × 1 （P13382） SULFATE ION × 15 ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 SULFATE ION × 19 ZINC ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 SULFATE ION × 15 ZINC ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 SULFATE ION × 16 ZINC ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase alpha subunit B × 1 （P38121） DNA polymerase alpha catalytic subunit A × 1 SULFATE ION × 15 ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3flo
Deposition date deposition_date	2008-12-19
Structure title title	Crystal 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 method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3flo__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3flo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3flo__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.75 Å
Rg (electron density)	27.54 Å
Total Rg	28.40 Å
Atom count	5009
Residues	616
Excluded volume	88702 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3flo__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3flo__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3flo__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3flo__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DNA polymerase alpha subunit B
Molecular weight formula_weight	51962.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	20656

KFRTMRQNLQEASDVLDDQIESFTKIIQNHYKLSPNDFADPTIQSQSEIYAVGRIVPDSPTYDKFLNPESLSLETSRMGGVGRRVRLDLSQVNELSFFLGQIVAFKGKNANGDYFTVNSILPLPYPNSPVSTSQELQEFQANLEGSSLKVIVTCGPYFANDNFSLELLQEFIDSINNEVKPHVLIMFGPFIDITHPLIASGKLPNFPQFKTQPKTLDELFLKLFTPILKTISPHIQTVLIPSTKDAISNHAAYPQASLIRKALQLPKRNFKCMANPSSFQINEIYFGCSNVDTFKDLKEVIKGGTTSSRYRLDRVSEHILQQRRYYPIFPGSIRTRIKPKDVSTKKETNDMESKEEKVYEHISGADLDVSYLGLTEFVGGFSPDIMIIPSELQHFARVVQNVVVINPGRFIRATGNRGSYAQITVQCPDLEDGKLTLVEGEEPVYLHNVWKRARVDLIAS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA polymerase alpha catalytic subunit A
Molecular weight formula_weight	273.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L

XXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA polymerase alpha catalytic subunit A
Molecular weight formula_weight	23981.2 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

NLQPLETTITDVERFKDTVTLELSCPSCDKRFPFGGIVSSNYYRVSYNGLQCKHCEQLFTPLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSVFGKRCLNDGCTGVMRYKYSDKQLYNQLLYFDSLFDCEKNKKQELKPIYLPDDLDYPKEQLTESSIKALTEQNRELMETGRSVVQKYLNDCGRRYVDMTSIFDFMLN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	65

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	571

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3floA02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3floB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily	20 — DNA Polymerase alpha, zinc finger

Domain ID domain_id	3floC02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3floD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily	20 — DNA Polymerase alpha, zinc finger

Domain ID domain_id	3floE02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3floF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily	20 — DNA Polymerase alpha, zinc finger

Domain ID domain_id	3floG02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3floH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3200 — Hypothetical protein af0941
Homologous superfamily homologous superfamily	20 — DNA Polymerase alpha, zinc finger

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Unit-cell length a length_a	85.411 Å
Unit-cell length b length_b	142.633 Å
Unit-cell length c length_c	175.255 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	31.900 Å
R factor r_factor	0.1920
R_work r_work	0.1910
R_free r_free	0.2180

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

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

DNA polymerase alpha subunit B

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase alpha catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3flo__assembly_1__model_1

3flo__assembly_1__model_1 | I(q)

3flo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

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

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

DNA polymerase alpha subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase alpha catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3flo__assembly_1__model_1

3flo__assembly_1__model_1 | I(q)

3flo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)