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2d7e

Crystal structure of N-terminal domain of PriA from E.coli

Method: X-RAY DIFFRACTION Dmax: 87.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

;Primosomal protein N' ;

Escherichia coli

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–105 Chain B； UniProt 1–105 Fragment：DNA binding domein No other associated polymer 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–105 Chain D； UniProt 1–105 Fragment：DNA binding domein No other associated polymer 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
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–105 Chain B； UniProt 1–105 Fragment：DNA binding domein No other associated polymer 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
4 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–105 Chain D； UniProt 1–105 Fragment：DNA binding domein No other associated polymer 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

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 2D7E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2D7G Crystal structure of the aa complex of the N-terminal domain of PriA Deposited 2005-11-21 Different construct Different oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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
9ZBT 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: heptameric
Chain H 1–732（732 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 3.22 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRIA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–105； UniProt 1–105 Author chain B； PDBConstruct 1–105； UniProt 1–105 Author chain C； PDBConstruct 1–105； UniProt 1–105 Author chain D； PDBConstruct 1–105； UniProt 1–105

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2d7e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2d7e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2d7e
Deposition date deposition_date2005-11-18
Structure title titleCrystal structure of N-terminal domain of PriA from E.coli
Keywords keywordsinter-twined, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.27 Å
Radius of gyration Rg (electron density) rg_electron26.72 Å
Forward intensity I(0) i031300100.00
Molecular weight molecular_weight46564.0 kDa
Excluded volume excluded_volume59814 ų
Envelope volume envelope_volume78068 ų
Hydration-shell volume shell_volume25481 ų
Envelope diameter envelope_diameter90.2 Å
Shell Rg shell_rg32.77 Å
Envelope Rg envelope_rg26.56 Å
Shape Rg shape_rg26.72 Å
Total Rg total_rg27.48 Å
Total atoms total_atoms3296
Residues n_residues417
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.9 Å
Rg (real space) rg_real27.34 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real3.1300e+07
I(0) uncertainty (real space) i0_real_error4.5990e+05
Rg (reciprocal space) rg_reciprocal27.32 Å
I(0) (reciprocal space) i0_reciprocal31300000.0000
Solution quality estimate total_estimate0.8977
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3 Å
Skewness Skewness skewness0.369
Kurtosis Kurtosis kurtosis-0.445
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6461000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.920
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id2d7eA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily60 — PriA, 3(prime) DNA-binding domain
Domain ID domain_id2d7eB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily60 — PriA, 3(prime) DNA-binding domain
Domain ID domain_id2d7eC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily60 — PriA, 3(prime) DNA-binding domain
Domain ID domain_id2d7eD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1440 — GIY-YIG endonuclease
Homologous superfamily homologous superfamily60 — PriA, 3(prime) DNA-binding domain
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8. Citations (2)

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9. Files and Curves (10)