3e0j

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta

Method: X-RAY DIFFRACTION

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

DNA polymerase subunit delta-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-3 × 1 （Q15054） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-3 × 1 （Q15054） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-3 × 1 （Q15054） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-3 × 1 （Q15054） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–476； UniProt 1–469 Author chain C； PDBConstruct 8–476； UniProt 1–469 Author chain E； PDBConstruct 8–476； UniProt 1–469 Author chain G； PDBConstruct 8–476； UniProt 1–469

DNA polymerase subunit delta-3

Homo sapiens

UniProt Q15054

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-2 × 1 （P49005） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-2 × 1 （P49005） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-2 × 1 （P49005） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase subunit delta-2 × 1 （P49005） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOD3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–144； UniProt 1–144 Author chain D； PDBConstruct 1–144； UniProt 1–144 Author chain F； PDBConstruct 1–144； UniProt 1–144 Author chain H； PDBConstruct 1–144； UniProt 1–144

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	3e0j
Deposition date deposition_date	2008-07-31
Structure title title	X-ray structure of the complex of regulatory subunits of human DNA polymerase delta
Keywords keywords	;DNA Polymerase Delta, p66 subunit, p50 subunit, human, DNA replication, DNA-directed DNA polymerase, Nucleotidyltransferase, Nucleus, Polymorphism, Transferase, Phosphoprotein ;; 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.

3e0j__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3e0j__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e0j__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.69 Å
Rg (electron density)	27.30 Å
Total Rg	27.90 Å
Atom count	4256
Residues	551
Excluded volume	75952 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e0j__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e0j__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3e0j__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3e0j__assembly_4__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	DNA polymerase subunit delta-2
Molecular weight formula_weight	52224.1 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	A,C,E,G
Atom count atom_count	17153

HHHHHHGMFSEQAAQRAHTLLSPPSANNATFARVPVATYTNSSQPFRLGERSFSRQYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFADLAPQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAEDDDLGGLGLGP

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 2 Entity 2 polymer

Description description	DNA polymerase subunit delta-3
Molecular weight formula_weight	16233.6 kDa
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

MADQLYLENIDEFVTDQNKIVTYKWLSYTLGVHVNQAKQMLYDYVERKRKENSGAQLHVTYLVSGSLIQNGHSCHKVAVVREDKLEAVKSKLAVTASIHVYSIQKAMLKDSGPLFNTDYDILKSNLQNCSKFSAIQCAAAVPRA

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3e0jA01
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	50 —

Domain ID domain_id	3e0jA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	430 —

Domain ID domain_id	3e0jB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
Homologous superfamily homologous superfamily	20 — DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain

Domain ID domain_id	3e0jC01
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	50 —

Domain ID domain_id	3e0jC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	430 —

Domain ID domain_id	3e0jD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
Homologous superfamily homologous superfamily	20 — DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain

Domain ID domain_id	3e0jE01
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	50 —

Domain ID domain_id	3e0jE02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	430 —

Domain ID domain_id	3e0jF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
Homologous superfamily homologous superfamily	20 — DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain

Domain ID domain_id	3e0jG01
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	50 —

Domain ID domain_id	3e0jG02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	430 —

Domain ID domain_id	3e0jH00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1030 — 50s Ribosomal Protein L17; Chain: A,
Homologous superfamily homologous superfamily	20 — DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain

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Unit-cell length a length_a	95.128 Å
Unit-cell length b length_b	248.535 Å
Unit-cell length c length_c	103.461 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.94 °
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	3.000 Å
Low-resolution limit resolution_low	29.890 Å
R factor r_factor	0.2570
R_work r_work	0.2570
R_free r_free	0.2810

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta

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

DNA polymerase subunit delta-2

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase subunit delta-3

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

3e0j__assembly_2__model_1

3e0j__assembly_2__model_1 | I(q)

3e0j__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta

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

DNA polymerase subunit delta-2

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 subunit delta-3

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

3e0j__assembly_2__model_1

3e0j__assembly_2__model_1 | I(q)

3e0j__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)