1jr3

Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III

Method: X-RAY DIFFRACTION

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

DNA polymerase III subunit gamma

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	DNA polymerase III, delta subunit × 1 （P28630） ;DNA polymerase III, delta' subunit ; × 1 （P28631） ZINC ION × 4 SULFATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3X_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–373； UniProt 1–373 Author chain B； PDBConstruct 1–373； UniProt 1–373 Author chain C； PDBConstruct 1–373； UniProt 1–373

DNA polymerase III, delta subunit

Escherichia coli

UniProt P28630

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	DNA polymerase III subunit gamma × 3 （P06710） ;DNA polymerase III, delta' subunit ; × 1 （P28631） ZINC ION × 4 SULFATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HOLA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–343； UniProt 1–343

;DNA polymerase III, delta' subunit ;

Escherichia coli

UniProt P28631

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	DNA polymerase III subunit gamma × 3 （P06710） DNA polymerase III, delta subunit × 1 （P28630） ZINC ION × 4 SULFATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HOLB_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–334； 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	1jr3
Deposition date deposition_date	2001-08-10
Structure title title	Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III
Keywords keywords	DNA Polymerase, Processivity, Processivity clamp, clamp loader, AAA+ ATPASE, 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.

1jr3__assembly_1__model_1

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

Download this curve (.dat)

1jr3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jr3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.39 Å
Rg (electron density)	39.39 Å
Total Rg	39.84 Å
Atom count	13845
Residues	1769
Excluded volume	247070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jr3__assembly_1__model_1`	pentameric （5）	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 (5)

Entity 1 Entity 1 polymer

Description description	DNA polymerase III subunit gamma
Molecular weight formula_weight	41510.9 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	13845

MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPEVPRQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA polymerase III, delta subunit
Molecular weight formula_weight	38745.6 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA polymerase III, delta' subunit ;
Molecular weight formula_weight	36980.5 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1jr3a1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1jr3a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1jr3b1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1jr3b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1jr3c1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1jr3c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1jr3d1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1jr3d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1jr3e1
Class class	a — All alpha proteins
Fold Fold fold	a.80 — post-AAA+ oligomerization domain-like
Superfamily Superfamily superfamily	a.80.1 — post-AAA+ oligomerization domain-like
Family Family family	a.80.1.1 — DNA polymerase III clamp loader subunits, C-terminal domain

Domain ID domain_id	d1jr3e2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (15 domains)

Domain ID domain_id	1jr3A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1jr3A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jr3A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1jr3B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1jr3B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jr3B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1jr3C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1jr3C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jr3C03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1jr3D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1jr3D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1jr3D03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1jr3E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1jr3E02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	1jr3E03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	95.698 Å
Unit-cell length b length_b	95.857 Å
Unit-cell length c length_c	285.410 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	500.000 Å
R factor r_factor	—
R_work r_work	0.2676
R_free r_free	0.3043

Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III

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

DNA polymerase III subunit gamma

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase III, delta subunit

State in the Current Structure

Other States of the Same Protein in the Database

;DNA polymerase III, delta' subunit ;

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

1jr3__assembly_1__model_1

1jr3__assembly_1__model_1 | I(q)

1jr3__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 (5)

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

6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (10 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III

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

DNA polymerase III subunit gamma

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, delta subunit

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, delta' subunit ;

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

1jr3__assembly_1__model_1

1jr3__assembly_1__model_1 | I(q)

1jr3__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 (5)

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

6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (10 domains)

CATH v4.4 (15 domains)

7. Citations (1)