9zbu

Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome

Method: ELECTRON MICROSCOPY

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

Replication restart protein PriB

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 3	DNA (36-MER) × 1 DNA (33-MER) × 1 DNA (11-MER) × 1 Replication restart protein DnaT × 7 （P0A8J2） Replication restart protein PriA × 1 （P17888） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIB_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 2–100 Author chain B； PDBConstruct 1–99； UniProt 2–100

Replication restart protein DnaT

Escherichia coli K-12

UniProt P0A8J2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 3	DNA (36-MER) × 1 DNA (33-MER) × 1 DNA (11-MER) × 1 Replication restart protein PriB × 2 （P07013） Replication restart protein PriA × 1 （P17888） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAT_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–154； UniProt 1–154 Author chain D； PDBConstruct 1–154； UniProt 1–154 Author chain E； PDBConstruct 1–154； UniProt 1–154 Author chain T； PDBConstruct 1–154； UniProt 1–154 Author chain W； PDBConstruct 1–154； UniProt 1–154 Author chain X； PDBConstruct 1–154； UniProt 1–154 Author chain Y； PDBConstruct 1–154； UniProt 1–154

Replication restart protein PriA

Escherichia coli K-12

UniProt P17888

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 3	DNA (36-MER) × 1 DNA (33-MER) × 1 DNA (11-MER) × 1 Replication restart protein PriB × 2 （P07013） Replication restart protein DnaT × 7 （P0A8J2） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIA_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain H； PDBConstruct 1–731； UniProt 2–732

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	9zbu
Deposition date deposition_date	2025-11-21
Structure title title	Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome
Keywords keywords	DNA replication, helicase, oligomer, DNA repair, REPLICATION; REPLICATION
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.

9zbu__assembly_1__model_1

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

Download this curve (.dat)

9zbu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9zbu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.80 Å
Rg (electron density)	46.75 Å
Total Rg	46.91 Å
Atom count	13223
Residues	1563
Excluded volume	230110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9zbu__assembly_1__model_1`	tridecameric （13）	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 (36-MER)
Molecular weight formula_weight	10955.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G
Atom count atom_count	13223

CCGCAGACTCATTTAGCCCTTATCCGTATTGCGGTC

Entity 2 Entity 2 polymer

Description description	DNA (33-MER)
Molecular weight formula_weight	10223.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

GACCGCAATACGGATAAGGGCTGAGCACGCCGA

Entity 3 Entity 3 polymer

Description description	DNA (11-MER)
Molecular weight formula_weight	3341.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Z

TCGGCGTGCTC

Entity 4 Entity 4 polymer

Description description	Replication restart protein PriB
Molecular weight formula_weight	10953.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELI

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Replication restart protein DnaT
Molecular weight formula_weight	16851.2 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,T,W,X,Y

MSSRVLTPDVVGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVTPARLAELLALEEKLARPGSDVALDDQLYQEPQAAPVAVPMGKFAMYPDWQPDADFIRLAALWGVALREPVTTEELASFIAYWQAEGKVFHHVQWQQKLARSLQIGRAS

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	Replication restart protein PriA
Molecular weight formula_weight	81634.6 kDa
EC 编号 ec_number	5.6.2.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

PVAHVALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQERIGIVVSVSDASELPLNELKAVVEVLDSEPVFTHSVWRLLLWAADYYHHPIGDVLFHALPILLRQGRPAANAPMWYWFATEQGQAVDLNSLKRSPKQQQALAALRQGKIWRDQVATLEFNDAALQALRKKGLCDLASETPEFSDWRTNYAVSGERLRLNTEQATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLKGQKVQAGLAPALITRMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHHLRCHHCDSQRPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPGVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWTSHVIVRAEDHNNQHAPLFLQQLRNLILSSPLADEKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIINGTLALINTIPDSRKVKWVLDVDPIEG

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Resolution resolution	3.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	212000

Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome

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

Replication restart protein PriB

State in the Current Structure

Other States of the Same Protein in the Database

Replication restart protein DnaT

State in the Current Structure

Other States of the Same Protein in the Database

Replication restart protein PriA

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

9zbu__assembly_1__model_1

9zbu__assembly_1__model_1 | I(q)

9zbu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (1)

Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome

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

Replication restart protein PriB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Replication restart protein DnaT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Replication restart protein PriA

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

9zbu__assembly_1__model_1

9zbu__assembly_1__model_1 | I(q)

9zbu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (1)