4iqj

Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome

Method: X-RAY DIFFRACTION

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

DNA polymerase III subunit alpha

Thermus aquaticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 8	;DNA (5'-D(PCPGPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPA)-3') ; × 3 ;DNA (5'-D(TPTPTPTPTPTPTPGPTPGPGPCPAPCPTPGPGPCPCPGPTPCPGPTPTPTPCPG)-3') ; × 4 ;DNA (5'-D(PCPGPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPAP*(DOC))-3') ; × 1 DNA polymerase III subunit gamma/tau × 4 （A0A0M9ACL9） ZINC ION × 12 MAGNESIUM ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3A_THEAQ
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–1220； UniProt 1–1220 Author chain B； PDBConstruct 1–1220； UniProt 1–1220 Author chain C； PDBConstruct 1–1220； UniProt 1–1220 Author chain D； PDBConstruct 1–1220； UniProt 1–1220

DNA polymerase III subunit gamma/tau

Thermus aquaticus

UniProt A0A0M9ACL9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 8	;DNA (5'-D(PCPGPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPA)-3') ; × 3 ;DNA (5'-D(TPTPTPTPTPTPTPGPTPGPGPCPAPCPTPGPGPCPCPGPTPCPGPTPTPTPCPG)-3') ; × 4 ;DNA (5'-D(PCPGPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPAP*(DOC))-3') ; × 1 DNA polymerase III subunit alpha × 4 （Q9XDH5） ZINC ION × 12 MAGNESIUM ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0M9ACL9_THEAQ
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 7–174； UniProt 373–540 Author chain N； PDBConstruct 7–174； UniProt 373–540 Author chain O； PDBConstruct 7–174； UniProt 373–540 Author chain P； PDBConstruct 7–174； UniProt 373–540

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	4iqj
Deposition date deposition_date	2013-01-11
Structure title title	Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome
Keywords keywords	;Polymerase, alpha subunit, TauC subunit, DNA replication, DNA-directed DNA Polymerase, Nucleotidyltransferase, 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.

4iqj__assembly_1__model_1

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

Download this curve (.dat)

4iqj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4iqj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	79.33 Å
Rg (electron density)	79.89 Å
Total Rg	79.71 Å
Atom count	45265
Residues	5402
Excluded volume	795650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4iqj__assembly_1__model_1`	hexadecameric （16）	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(PCPGPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPA)-3') ;
Molecular weight formula_weight	6138.0 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G,K
Atom count atom_count	45265

CGAAACGACGGCCAGTGCCA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPTPTPTPTPTPTPGPTPGPGPCPAPCPTPGPGPCPCPGPTPCPGPTPTPTPCPG)-3') ;
Molecular weight formula_weight	8591.5 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H,J,L

TTTTTTTGTGGCACTGGCCGTCGTTTCG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PCPGPAPAPAPCPGPAPCPGPGPCPCPAPGPTPGPCPCPAP*(DOC))-3') ;
Molecular weight formula_weight	6411.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

CGAAACGACGGCCAGTGCCAC

Entity 4 Entity 4 polymer

Description description	DNA polymerase III subunit alpha
Molecular weight formula_weight	137579.4 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,B,C,D

MGSKLKFAHLHQHTQFSLLDGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKRGKGLDGGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDREILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNDGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEFYVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPLPEGRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLGTMPPHGDERALAEALARVEEKAWEELRKRLPPLEGVREWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEAIQVVPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGIPVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPLVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKGEELRVLAQAVWTLEEVLEAPKALEVEVDHALLDEKGVARLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVFLQGNGGGPKEEVVPF

Source Source

Source organism organism	Thermus aquaticus
NCBI taxonomy ID ncbi_taxonomy_id	271
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA polymerase III subunit gamma/tau
Molecular weight formula_weight	19600.3 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	M,N,O,P

HHHHHHKAGEAQDLAEGWRAFLEALKPTLRAFVREARPHLEGKTLVLRFPESKAFHHKKAEEQKAHLLPLARAQFGVEELAFVLEKKSLSGASPPPPTKPVPPREAPPPVAAPPPEPEPPLEDPPWEAEEGEDPSEELRRLARLLGGRLLWVRKPKAPEAEEPVSEDGIGGNGIMPP

Source Source

Source organism organism	Thermus aquaticus
NCBI taxonomy ID ncbi_taxonomy_id	271
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4iqjA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	4iqjA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1600 — Bacterial DNA polymerase III alpha subunit, thumb domain

Domain ID domain_id	4iqjB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	4iqjB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1600 — Bacterial DNA polymerase III alpha subunit, thumb domain

Domain ID domain_id	4iqjC01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	4iqjC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1600 — Bacterial DNA polymerase III alpha subunit, thumb domain

Domain ID domain_id	4iqjD01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	4iqjD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1600 — Bacterial DNA polymerase III alpha subunit, thumb domain

Domain ID domain_id	4iqjM02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	4iqjN02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	4iqjO02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	4iqjP02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	188.530 Å
Unit-cell length b length_b	94.970 Å
Unit-cell length c length_c	204.080 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.97 °
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	3.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2663
R_work r_work	0.2643
R_free r_free	0.3047

Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome

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

DNA polymerase III subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase III subunit gamma/tau

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

4iqj__assembly_1__model_1

4iqj__assembly_1__model_1 | I(q)

4iqj__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (3)

Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome

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

DNA polymerase III subunit alpha

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 III subunit gamma/tau

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

4iqj__assembly_1__model_1

4iqj__assembly_1__model_1 | I(q)

4iqj__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (3)