SAXSdb — 9zbt

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

Replication restart protein DnaT

Escherichia coli K-12

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 4 DNA 3 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain D； UniProt 1–179	Not recorded	Replication restart protein PriB × 2 （P07013） DNA (33-MER) × 1 ;Primosomal protein N' ; × 1 （P17888） DNA (33-MER) × 1 DNA (11-MER) × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.22 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZBT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RU8 DnaT C-terminal domain Deposited 2014-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 89–179（91 aa） Fragment：ssDNA binding domain, UNP residues 89-179	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] DnaT-1, 20 mM HEPES-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.1 mM [U-99% 15N] DnaT-3, 20 mM HEPES-4, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4OU6 Crystal structure of DnaT84-153-dT10 ssDNA complex form 1 Deposited 2014-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 5 PDB declaration: hexameric	Chain A 84–159（76 aa） Fragment：UNP RESIDUES 84-159 Chain B 84–159（76 aa） Fragment：UNP RESIDUES 84-159 Chain C 84–159（76 aa） Fragment：UNP RESIDUES 84-159 Chain D 84–159（76 aa） Fragment：UNP RESIDUES 84-159 Chain E 84–159（76 aa） Fragment：UNP RESIDUES 84-159	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.96 Å R-free 0.228
4OU7 Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode Deposited 2014-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 5 PDB declaration: hexameric	Chain A 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain B 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain C 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain D 84–154（71 aa） Fragment：UNP RESIDUES 84-154 Chain E 84–154（71 aa） Fragment：UNP RESIDUES 84-154	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.83 Å R-free 0.238
9ZBU Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome Deposited 2025-11-21	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric	Chain C 1–154（154 aa） Chain D 1–154（154 aa） Chain E 1–154（154 aa） Chain T 1–154（154 aa） Chain W 1–154（154 aa） Chain X 1–154（154 aa） Chain Y 1–154（154 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DNAT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–179； UniProt 1–179

Replication restart protein PriB

Escherichia coli K-12

UniProt P07013

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 4 DNA 3 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain A； UniProt 1–104 Chain B； UniProt 1–104	Not recorded	Replication restart protein DnaT × 1 （P0A8J2） DNA (33-MER) × 1 ;Primosomal protein N' ; × 1 （P17888） DNA (33-MER) × 1 DNA (11-MER) × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.22 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZBT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TXY E. coli PriB Deposited 2004-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–103（103 aa） Chain B 1–103（103 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.285
1V1Q Crystal structure of PriB- a primosomal DNA replication protein of Escherichia coli Deposited 2004-04-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Mutation：YES Mutation：YES	CYS CYSTEINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；pH 5.70	Resolution 2.10 Å R-free 0.263
1WOC Crystal structure of PriB Deposited 2004-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–103（103 aa） Chain B 1–103（103 aa） Chain C 1–103（103 aa） Chain D 1–103（103 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25%(v/v) MPD, 50mM Magnesium Chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.276
1WOC Crystal structure of PriB Deposited 2004-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–103（103 aa） Chain D 1–103（103 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25%(v/v) MPD, 50mM Magnesium Chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.276
1WOC Crystal structure of PriB Deposited 2004-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–103（103 aa） Chain C 1–103（103 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25%(v/v) MPD, 50mM Magnesium Chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.276
2CCZ Crystal structure of E. coli primosomol protein PriB bound to ssDNA Deposited 2006-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–103（103 aa） Chain B 1–103（103 aa）	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.70 Å R-free 0.284
2PNH Escherichia coli PriB E39A variant Deposited 2007-04-24	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Mutation：E39A Mutation：E39A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；8% polyethylene glycol 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.276
8FAK DNA replication fork binding triggers structural changes in the PriA DNA helicase that regulate the PriA-PriB replication restart pathway in E. coli Deposited 2022-11-28	Different oligomeric state Different experimental conditions	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
9ZBU Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome Deposited 2025-11-21	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric	Chain A 2–100（99 aa） Chain B 2–100（99 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRIB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain B； PDBConstruct 1–104； UniProt 1–104

;Primosomal protein N' ;

Escherichia coli K-12

UniProt P17888

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 4 DNA 3 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain H； UniProt 1–732	Not recorded	Replication restart protein DnaT × 1 （P0A8J2） Replication restart protein PriB × 2 （P07013） DNA (33-MER) × 1 DNA (33-MER) × 1 DNA (11-MER) × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.22 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZBT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–105（105 aa） Fragment：DNA binding domein Chain B 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–105（105 aa） Fragment：DNA binding domein Chain D 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–105（105 aa） Fragment：DNA binding domein Chain B 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7E Crystal structure of N-terminal domain of PriA from E.coli Deposited 2005-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–105（105 aa） Fragment：DNA binding domein Chain D 1–105（105 aa） Fragment：DNA binding domein	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；0.1M sodium citrate, 0.3M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.292
2D7G Crystal structure of the aa complex of the N-terminal domain of PriA Deposited 2005-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–105（105 aa） Fragment：residues 1-105 Chain B 1–105（105 aa） Fragment：residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；12% PEG 6000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309
2D7G Crystal structure of the aa complex of the N-terminal domain of PriA Deposited 2005-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 1–105（105 aa） Fragment：residues 1-105 Chain D 1–105（105 aa） Fragment：residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；12% PEG 6000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309
2D7H Crystal structure of the ccc complex of the N-terminal domain of PriA Deposited 2005-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: pentameric	Chain A 1–105（105 aa） Fragment：residues 1-105 Chain B 1–105（105 aa） Fragment：residues 1-105 Chain C 1–105（105 aa） Fragment：residues 1-105 Chain D 1–105（105 aa） Fragment：residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.293
2DWL Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–105（105 aa） Fragment：Residues 1-105 Chain B 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.302
2DWL Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain C 1–105（105 aa） Fragment：Residues 1-105 Chain D 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.302
2DWM Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–105（105 aa） Fragment：Residues 1-105 Chain B 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.318
2DWM Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 1–105（105 aa） Fragment：Residues 1-105 Chain D 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；293 K；0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.318
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–105（105 aa） Fragment：Residues 1-105 Chain B 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain C 1–105（105 aa） Fragment：Residues 1-105 Chain D 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–105（105 aa） Fragment：Residues 1-105 Chain B 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
2DWN Crystal structure of the PriA protein complexed with oligonucleotides Deposited 2006-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain C 1–105（105 aa） Fragment：Residues 1-105 Chain D 1–105（105 aa） Fragment：Residues 1-105	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.35 Å R-free 0.333
6DCR E. coli PriA helicase winged helix domain deletion protein Deposited 2018-05-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–732（732 aa）	Mutation：delta 114-174	ZN ZINC ION × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride	Resolution 1.98 Å R-free 0.215
6DCR E. coli PriA helicase winged helix domain deletion protein Deposited 2018-05-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–732（732 aa）	Mutation：delta 114-174	ZN ZINC ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride	Resolution 1.98 Å R-free 0.215
8FAK DNA replication fork binding triggers structural changes in the PriA DNA helicase that regulate the PriA-PriB replication restart pathway in E. coli Deposited 2022-11-28	Different oligomeric state Different experimental conditions	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric	Chain H 1–732（732 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
9ZBU Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome Deposited 2025-11-21	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric	Chain H 2–732（731 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

9 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRIA_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–732； UniProt 1–732

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	9zbt
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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.41 Å
Radius of gyration Rg (electron density) rg_electron	39.09 Å
Forward intensity I(0) i0	362605000.00
Molecular weight molecular_weight	137640.0 kDa
Excluded volume excluded_volume	165480 Å³
Envelope volume envelope_volume	240060 Å³
Hydration-shell volume shell_volume	53645 Å³
Envelope diameter envelope_diameter	147.4 Å
Shell Rg shell_rg	42.45 Å
Envelope Rg envelope_rg	38.87 Å
Shape Rg shape_rg	39.05 Å
Total Rg total_rg	39.41 Å
Total atoms total_atoms	9594
Residues n_residues	1098
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	138.6 Å
Rg (real space) rg_real	39.60 Å
Rg uncertainty (real space) rg_real_error	1.66 Å
I(0) (real space) i0_real	3.6260e+08
I(0) uncertainty (real space) i0_real_error	7.4240e+06
Rg (reciprocal space) rg_reciprocal	39.48 Å
I(0) (reciprocal space) i0_reciprocal	362600000.0000
Solution quality estimate total_estimate	0.8584
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.0 Å
Skewness Skewness skewness	0.488
Kurtosis Kurtosis kurtosis	-0.071
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34840000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.866

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Replication restart protein DnaT
Molecular weight formula_weight	19474.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	9594

MSSRVLTPDVVGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVTPARLAELLALEEKLARPGSDVALDDQLYQEPQAAPVAVPMGKFAMYPDWQPDADFIRLAALWGVALREPVTTEELASFIAYWQAEGKVFHHVQWQQKLARSLQIGRASNGGLPKRDVNTVSEPDSQIPPGFRG

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Replication restart protein PriB
Molecular weight formula_weight	11459.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSGD

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	DNA (33-MER)
Molecular weight formula_weight	12206.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

GCCGCAGACTCATTTAGCCCTTATCCGTATTGCGGTCTCG

Entity 4 Entity 4 polymer

Description description	;Primosomal protein N' ;
Molecular weight formula_weight	81765.8 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MPVAHVALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQERIGIVVSVSDASELPLNELKAVVEVLDSEPVFTHSVWRLLLWAADYYHHPIGDVLFHALPILLRQGRPAANAPMWYWFATEQGQAVDLNSLKRSPKQQQALAALRQGKIWRDQVATLEFNDAALQALRKKGLCDLASETPEFSDWRTNYAVSGERLRLNTEQATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLKGQKVQAGLAPALITRMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHHLRCHHCDSQRPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPGVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWTSHVIVRAEDHNNQHAPLFLQQLRNLILSSPLADEKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIINGTLALINTIPDSRKVKWVLDVDPIEG

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	DNA (33-MER)
Molecular weight formula_weight	12400.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CGAGACCGCAATACGGATAAGGGCTGAGCACGCCGACGAA

Entity 6 Entity 6 polymer

Description description	DNA (11-MER)
Molecular weight formula_weight	4567.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Z

TTCGTCGGCGTGCTC

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

▶

8. Citations (1)

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

Resolution resolution	3.22 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	857000

fit	/app/data/saxs_computation/zb/9zbt/9zbt.fit
pddf	/app/data/pr_computation/zb/9zbt/9zbt.pr.out
profile	/app/data/saxs_computation/zb/9zbt/9zbt.dat

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 DnaT

State in the Current Structure

Other States of the Same Protein in the Database

Replication restart protein PriB

State in the Current Structure

Other States of the Same Protein in the Database

;Primosomal protein N' ;

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)