3gv5

Human DNA polymerase iota in complex with T template DNA and incoming ddADP

Method: X-RAY DIFFRACTION

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

DNA polymerase iota

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	5'-D(GPTPGPGPAPTPGPAPG)-3' × 1 5'-D(PCPAPTPTPCPTPCPAPTPCPCPAPC)-3' × 1 CALCIUM ION × 4 GLYCEROL × 1 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(GPTPGPGPAPTPGPAPG)-3' × 1 5'-D(PCPAPTPTPCPTPCPAPTPCPCPAPC)-3' × 1 CALCIUM ION × 4 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLI_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–420； UniProt 1–420 Author chain D； PDBConstruct 1–420； UniProt 1–420

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	3gv5
Deposition date deposition_date	2009-03-30
Structure title title	Human DNA polymerase iota in complex with T template DNA and incoming ddADP
Keywords keywords	;Y-family polymerase, polymerase iota, error prone replication, DNA damage, DNA repair, DNA replication, DNA synthesis, DNA-binding, DNA-directed DNA polymerase, Magnesium, Metal-binding, Mutator protein, Nucleotidyltransferase, Nucleus, Schiff base, Transferase, 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.

3gv5__assembly_1__model_1

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

Download this curve (.dat)

3gv5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gv5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.76 Å
Rg (electron density)	23.45 Å
Total Rg	24.19 Å
Atom count	3471
Residues	390
Excluded volume	61207 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gv5__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gv5__assembly_2__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 polymerase iota
Molecular weight formula_weight	47590.1 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	7703

MELADVGAAASSQGVHDQVLPTPNASSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLVGSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEELLASLLNRVCQDGRKPHTVRLIIRRYSSEKHYGRESRQCPIPSHVIQKLGTGNYDVMTPMVDILMKLFRNMVNVKMPFHLTLLSVCFCNLKALNTAK

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 2 Entity 2 polymer

Description description	5'-D(GPTPGPGPAPTPGPAP*G)-3'
Molecular weight formula_weight	2835.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P,E

GTGGATGAG

Entity 3 Entity 3 polymer

Description description	5'-D(PCPAPTPTPCPTPCPAPTPCPCPAP*C)-3'
Molecular weight formula_weight	3846.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T,F

CATTCTCATCCAC

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	395.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	737

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3gv5b1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain

Domain ID domain_id	d3gv5b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain
Superfamily Superfamily superfamily	d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain
Family Family family	d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain

Domain ID domain_id	d3gv5d1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain

Domain ID domain_id	d3gv5d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain
Superfamily Superfamily superfamily	d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain
Family Family family	d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain

CATH v4.4 (8 domains)

Domain ID domain_id	3gv5B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	3gv5B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3gv5B03
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	3gv5B04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	100 — DNA polymerase, Y-family, little finger domain

Domain ID domain_id	3gv5D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	3gv5D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3gv5D03
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	3gv5D04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	100 — DNA polymerase, Y-family, little finger domain

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Unit-cell length a length_a	140.160 Å
Unit-cell length b length_b	71.750 Å
Unit-cell length c length_c	127.420 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	51.570 Å
R factor r_factor	0.2060
R_work r_work	0.2050
R_free r_free	0.2530

Human DNA polymerase iota in complex with T template DNA and incoming ddADP

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

DNA polymerase iota

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

3gv5__assembly_1__model_1

3gv5__assembly_1__model_1 | I(q)

3gv5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Human DNA polymerase iota in complex with T template DNA and incoming ddADP

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

DNA polymerase iota

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

3gv5__assembly_1__model_1

3gv5__assembly_1__model_1 | I(q)

3gv5__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)