SAXSdb — 8ice

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

PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(CPAPTPTPAPGPAPA)-3') ; × 1 ;DNA (5'-D(TPCPTPAPAPTPGPA)-3') ; × 1 CADMIUM ION × 2 SODIUM ION × 2 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOB_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 2–335； UniProt 1–334

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	8ice
Deposition date deposition_date	1996-04-19
Structure title title	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CDCL2 (1 MILLIMOLAR)
Keywords keywords	;DNA-DIRECTED DNA POLYMERASE, DNA REPLICATION, DNA REPAIR, NUCLEOTIDYLTRANSFERASE, COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA, TRANSFERASE-DNA complex ;; TRANSFERASE/DNA
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.

8ice__assembly_1__model_1

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

Download this curve (.dat)

8ice__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ice__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.62 Å
Rg (electron density)	23.30 Å
Total Rg	24.07 Å
Atom count	2926
Residues	343
Excluded volume	51267 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ice__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(CPAPTPTPAPGPAPA)-3') ;
Molecular weight formula_weight	2434.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T
Atom count atom_count	3064

CATTAGAA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPTPAPAPTPGPA)-3') ;
Molecular weight formula_weight	2425.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

TCTAATGA

Entity 3 Entity 3 polymer

Description description	PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))
Molecular weight formula_weight	38241.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d8icea1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.6 — DNA polymerase beta, N-terminal domain-like
Family Family family	a.60.6.1 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	d8icea3
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.12 — PsbU/PolX domain-like
Family Family family	a.60.12.1 — DNA polymerase beta-like, second domain

Domain ID domain_id	d8icea4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.218 — Nucleotidyltransferase
Superfamily Superfamily superfamily	d.218.1 — Nucleotidyltransferase
Family Family family	d.218.1.2 — DNA polymerase beta-like

CATH v4.4 (4 domains)

Domain ID domain_id	8iceA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	8iceA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	8iceA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	8iceA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

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7. Citations (8)

Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.

Biochemistry (1996)

PMID: 8841120 · DOI: 10.1021/bi960790i PRIMARY

;Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity ;

Biochemistry (1996)

A Structural Basis for Metal Ion Mutagenicity and Nucleotide Selectivity in Human DNA Polymerase Beta

Biochemistry (1996)

Polymerase Structures and Mechanism

Science (1994)

Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP

Science (1994)

Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism

Science (1994)

Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates

To be Published

The Role of Thumb Movement and Template Bending in Polymerase Fidelity

To be Published

Unit-cell length a length_a	178.260 Å
Unit-cell length b length_b	57.756 Å
Unit-cell length c length_c	48.255 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1710
R_work r_work	—
R_free r_free	—

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CDCL2 (1 MILLIMOLAR)

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

PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))

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

8ice__assembly_1__model_1

8ice__assembly_1__model_1 | I(q)

8ice__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (8)

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CDCL2 (1 MILLIMOLAR)

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

PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))

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

8ice__assembly_1__model_1

8ice__assembly_1__model_1 | I(q)

8ice__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (8)