3glf

Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA

Method: X-RAY DIFFRACTION

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

DNA polymerase III subunit delta

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase III subunit tau × 3 （P06710） ;DNA polymerase III subunit delta' ; × 1 （P28631） ;DNA (5'-D(TPTPTPTPTPTPAPTPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPAPTP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 3 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 3 ZINC ION × 4	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase III subunit tau × 3 （P06710） ;DNA polymerase III subunit delta' ; × 1 （P28631） ;DNA (5'-D(TPTPTPTPTPTPAPTPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPAPTP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 3 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 3 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

DNA polymerase III subunit tau

Escherichia coli

UniProt P06710

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase III subunit delta × 1 （P28630） ;DNA polymerase III subunit delta' ; × 1 （P28631） ;DNA (5'-D(TPTPTPTPTPTPAPTPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPAPTP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 3 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 3 ZINC ION × 4	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase III subunit delta × 1 （P28630） ;DNA polymerase III subunit delta' ; × 1 （P28631） ;DNA (5'-D(TPTPTPTPTPTPAPTPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPAPTP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 3 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 3 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3X_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 23–395； UniProt 1–373 Author chain C； PDBConstruct 23–395； UniProt 1–373 Author chain D； PDBConstruct 23–395； UniProt 1–373 Author chain G； PDBConstruct 23–395； UniProt 1–373 Author chain H； PDBConstruct 23–395； UniProt 1–373 Author chain I； PDBConstruct 23–395； UniProt 1–373

;DNA polymerase III subunit delta' ;

Escherichia coli

UniProt P28631

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase III subunit delta × 1 （P28630） DNA polymerase III subunit tau × 3 （P06710） ;DNA (5'-D(TPTPTPTPTPTPAPTPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPAPTP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 3 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 3 ZINC ION × 4	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase III subunit delta × 1 （P28630） DNA polymerase III subunit tau × 3 （P06710） ;DNA (5'-D(TPTPTPTPTPTPAPTPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPAPTP*A)-3') ; × 1 ADENOSINE-5'-DIPHOSPHATE × 3 BERYLLIUM TRIFLUORIDE ION × 3 MAGNESIUM ION × 3 ZINC ION × 4	Consistent with all polymers

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 Author chain J； 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	3glf
Deposition date deposition_date	2009-03-12
Structure title title	Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA
Keywords keywords	;AAA+ ATPase, Clamp Loader, Gamma Complex, Replication, DNA replication, DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase, ATP-binding, Nucleotide-binding, 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.

3glf__assembly_1__model_1

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

Download this curve (.dat)

3glf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3glf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.99 Å
Rg (electron density)	38.31 Å
Total Rg	38.72 Å
Atom count	14323
Residues	1782
Excluded volume	253750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3glf__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3glf__assembly_2__model_1`	heptameric （7）	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 (9)

Entity 1 Entity 1 polymer

Description description	DNA polymerase III subunit delta
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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	28758

MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA polymerase III subunit tau
Molecular weight formula_weight	43955.5 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D,G,H,I

MGSSHHHHHHSSGLEVLFQGPHMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPEVPRQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA polymerase III subunit delta' ;
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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J

MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(TPTPTPTPTPTPAPTPAPGPGPCPCPAP*G)-3') ;
Molecular weight formula_weight	4590.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K,M

TTTTTTATAGGCCAG

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(CPTPGPGPCPCPTPAPTPA)-3') ;
Molecular weight formula_weight	3020.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L,N

CTGGCCTATA

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 30 domains

CATH v4.4 (30 domains)

Domain ID domain_id	3glfA01
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	3glfA02
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	3glfA03
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	3glfB01
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	3glfB02
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	3glfB03
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	3glfC01
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	3glfC02
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	3glfC03
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	3glfD01
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	3glfD02
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	3glfD03
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	3glfE01
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	3glfE02
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	3glfE03
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	3glfF01
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	3glfF02
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	3glfF03
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	3glfG01
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	3glfG02
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	3glfG03
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	3glfH01
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	3glfH02
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	3glfH03
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	3glfI01
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	3glfI02
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	3glfI03
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	3glfJ01
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	3glfJ02
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	3glfJ03
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	100.264 Å
Unit-cell length b length_b	219.947 Å
Unit-cell length c length_c	273.150 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	24

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

Resolution resolution	3.388 Å
Low-resolution limit resolution_low	49.970 Å
R factor r_factor	0.2234
R_work r_work	0.2214
R_free r_free	0.2604

Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA

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

DNA polymerase III subunit delta

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 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

;DNA polymerase III subunit delta' ;

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

3glf__assembly_1__model_1

3glf__assembly_1__model_1 | I(q)

3glf__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 (9)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 30 domains

CATH v4.4 (30 domains)

7. Citations (1)