9oyh

Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state

Method: ELECTRON MICROSCOPY

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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 9 DNA 2	DNA polymerase III subunit tau × 3 （P06710） ;DNA polymerase III subunit delta' ; × 1 （P28631） Beta sliding clamp × 2 （P0A990） 10-nt gapped DNA template strand × 1 10-nt gapped DNA primer strand 1 × 1 DNA polymerase III subunit psi × 1 （P28632） DNA polymerase III subunit chi × 1 （P28905） ZINC ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	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

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 9 DNA 2	DNA polymerase III subunit delta × 1 （P28630） ;DNA polymerase III subunit delta' ; × 1 （P28631） Beta sliding clamp × 2 （P0A990） 10-nt gapped DNA template strand × 1 10-nt gapped DNA primer strand 1 × 1 DNA polymerase III subunit psi × 1 （P28632） DNA polymerase III subunit chi × 1 （P28905） ZINC ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	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 1–643； UniProt 1–643 Author chain C； PDBConstruct 1–643； UniProt 1–643 Author chain D； PDBConstruct 1–643； UniProt 1–643

;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 9 DNA 2	DNA polymerase III subunit delta × 1 （P28630） DNA polymerase III subunit tau × 3 （P06710） Beta sliding clamp × 2 （P0A990） 10-nt gapped DNA template strand × 1 10-nt gapped DNA primer strand 1 × 1 DNA polymerase III subunit psi × 1 （P28632） DNA polymerase III subunit chi × 1 （P28905） ZINC ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	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

Beta sliding clamp

Escherichia coli

UniProt P0A990

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA polymerase III subunit delta × 1 （P28630） DNA polymerase III subunit tau × 3 （P06710） ;DNA polymerase III subunit delta' ; × 1 （P28631） 10-nt gapped DNA template strand × 1 10-nt gapped DNA primer strand 1 × 1 DNA polymerase III subunit psi × 1 （P28632） DNA polymerase III subunit chi × 1 （P28905） ZINC ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3B_ECO57
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–366； UniProt 1–366 Author chain G； PDBConstruct 1–366； UniProt 1–366

DNA polymerase III subunit psi

Escherichia coli

UniProt P28632

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA polymerase III subunit delta × 1 （P28630） DNA polymerase III subunit tau × 3 （P06710） ;DNA polymerase III subunit delta' ; × 1 （P28631） Beta sliding clamp × 2 （P0A990） 10-nt gapped DNA template strand × 1 10-nt gapped DNA primer strand 1 × 1 DNA polymerase III subunit chi × 1 （P28905） ZINC ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HOLD_ECOLI
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain J； PDBConstruct 1–137； UniProt 1–137

DNA polymerase III subunit chi

Escherichia coli

UniProt P28905

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA polymerase III subunit delta × 1 （P28630） DNA polymerase III subunit tau × 3 （P06710） ;DNA polymerase III subunit delta' ; × 1 （P28631） Beta sliding clamp × 2 （P0A990） 10-nt gapped DNA template strand × 1 10-nt gapped DNA primer strand 1 × 1 DNA polymerase III subunit psi × 1 （P28632） ZINC ION × 4 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HOLC_ECOLI
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain L； PDBConstruct 1–146； UniProt 2–147

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	9oyh
Deposition date deposition_date	2025-06-04
Structure title title	Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state
Keywords keywords	;DNA replication, DNA damage repair, clamp loading complex, clamp beta, clamp loader DnaX-complex, REPLICATION, REPLICATION-DNA complex ;; REPLICATION/DNA
Experimental Method method	ELECTRON MICROSCOPY

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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.

9oyh__assembly_1__model_1

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

Download this curve (.dat)

9oyh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9oyh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.91 Å
Rg (electron density)	47.44 Å
Total Rg	47.58 Å
Atom count	22701
Residues	2823
Excluded volume	401370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9oyh__assembly_1__model_1`	11-meric （11）	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 (11)

Entity 1 Entity 1 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	22701

MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

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 subunit tau
Molecular weight formula_weight	71228.6 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	B,C,D

MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPEVPRQSFAPVAPTAVMTPTQVPPQPQSAPQQAPTVPLPETTSQVLAARQQLQRVQGATKAKKSEPAAATRARPVNNAALERLASVTDRVQARPVPSALEKAPAKKEAYRWKATTPVMQQKEVVATPKALKKALEHEKTPELAAKLAAEAIERDPWAAQVSQLSLPKLVEQVALNAWKEESDNAVCLHLRSSQRHLNNRGAQQKLAEALSMLKGSTVELTIVEDDNPAVRTPLEWRQAIYEEKLAQARESIIADNNIQTLRRFFDAELDEESIRPI

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 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	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 polymer

Description description	Beta sliding clamp
Molecular weight formula_weight	40630.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G

MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL

Source Source

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

Entity 5 Entity 5 polymer

Description description	10-nt gapped DNA template strand
Molecular weight formula_weight	15389.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

CGGTATAGGCGATACGAATCTTTTTTTTTTCCGTATAGCCGTAGCGAGCC

Source Source

Source organism organism	DNA molecule
NCBI taxonomy ID ncbi_taxonomy_id	2853804
Host organism host_organism	DNA molecule

Entity 6 Entity 6 polymer

Description description	10-nt gapped DNA primer strand 1
Molecular weight formula_weight	6151.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

GGCTCGCTACGGCTATACGG

Source Source

Source organism organism	DNA molecule
NCBI taxonomy ID ncbi_taxonomy_id	2853804
Host organism host_organism	DNA molecule

Entity 7 Entity 7 polymer

Description description	DNA polymerase III subunit psi
Molecular weight formula_weight	15188.3 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	J

MTSRRDWQLQQLGITQWSLRRPGALQGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRND

Source Source

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

Entity 8 Entity 8 polymer

Description description	DNA polymerase III subunit chi
Molecular weight formula_weight	16522.5 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	L

KNATFYLLDNDTTVDGLSAVEQLVCEIAAERWRSGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEGPRGGAPVEIAWPQKRSSSRRDILISLRTSFADFATAFTEVVDFVPYEDSLKQLARERYKAYRVAGFNLNTATWK

Source Source

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

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	4

Entity 10 Entity 10 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.540 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.54 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	473295

Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state

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

Beta sliding clamp

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 psi

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 chi

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

9oyh__assembly_1__model_1

9oyh__assembly_1__model_1 | I(q)

9oyh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer