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8v9s

Distinct Quaternary States, Intermediates, and Autoinhibition During Loading of the DnaB-Replicative Helicase by the Phage Lambda P Helicase Loader

Method: X-RAY DIFFRACTION Dmax: 44.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Replication protein P

Escherichia phage Lambda

UniProt P03689

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 105–210 Fragment：residues 105 to 210 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298.15 K；Crystals were prepared using the sitting drop vapor diffusion method by mixing either 0.1, or 0.2, or 0.4 uL of the protein solution and 0.2 uL of a series of commercially available crystallization screens (Qiagen). Optimized crystals for X-ray diffraction were grown at room temperature in a buffer consisting of 3 M to 4 M NaCl with 0.1 M HEPES-NaOH, pH 7 to 8 and required 7 days to form. Resolution 1.86 Å R-free 0.244

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 8V9S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6BBM Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex Deposited 2017-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain V 1–107（107 aa）
Chain W 1–107（107 aa）
Chain X 1–107（107 aa）
Chain Y 1–107（107 aa）
Chain Z 1–107（107 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Concentrated BP sample (18mg/mL) was diluted with freshly prepared buffer to desired concentration (~1.5 micromolar) for grid preparation.
cryo-EM vitrification conditions Cryogen ETHANE；3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane.
Resolution 4.10 Å
8V9T Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio Deposited 2023-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain V 1–233（233 aa）
Chain W 1–233（233 aa）
Chain X 1–233（233 aa）
Chain Y 1–233（233 aa）
Chain Z 1–233（233 aa）
Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.
Resolution 2.84 Å
9OA1 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio. Deposited 2025-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain V 1–233（233 aa）
Chain W 1–233（233 aa）
Chain X 1–233（233 aa）
Chain Y 1–233（233 aa）
Chain Z 1–233（233 aa）
Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.
Resolution 2.66 Å
9OA2 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:6 stoichiometry ratio. Deposited 2025-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain U 1–233（233 aa）
Chain V 1–233（233 aa）
Chain W 1–233（233 aa）
Chain X 1–233（233 aa）
Chain Y 1–233（233 aa）
Chain Z 1–233（233 aa）
Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E Mutation：K2E ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE；Protein BP (1.5 uM), ssDNA (1.875 uM), and LO-156-299-NHis (2.25 uM) was mixed at 1.25 and 1.5 molar excess, respectively. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.
Resolution 3.85 Å

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

View Construct and Data Evidence
UniProt name VRPP_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–114； UniProt 105–210

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 8v9s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8v9s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8v9s
Deposition date deposition_date2023-12-09
Structure title titleDistinct Quaternary States, Intermediates, and Autoinhibition During Loading of the DnaB-Replicative Helicase by the Phage Lambda P Helicase Loader
Keywords keywordshexameric DnaB helicase, replicative loader, Phage Lambda P helicase loader, bacterial DNA replication initiation, REPLICATION; REPLICATION
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_guinier13.37 Å
Radius of gyration Rg (electron density) rg_electron12.09 Å
Forward intensity I(0) i01857290.00
Molecular weight molecular_weight8775.0 kDa
Excluded volume excluded_volume10727 ų
Envelope volume envelope_volume12147 ų
Hydration-shell volume shell_volume8920 ų
Envelope diameter envelope_diameter45.2 Å
Shell Rg shell_rg17.16 Å
Envelope Rg envelope_rg12.53 Å
Shape Rg shape_rg12.11 Å
Total Rg total_rg13.27 Å
Total atoms total_atoms607
Residues n_residues71
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 dmax44.8 Å
Rg (real space) rg_real13.32 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real1.8570e+06
I(0) uncertainty (real space) i0_real_error1.9270e+04
Rg (reciprocal space) rg_reciprocal13.33 Å
I(0) (reciprocal space) i0_reciprocal1857000.0000
Solution quality estimate total_estimate0.7958
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.9 Å
Skewness Skewness skewness0.225
Kurtosis Kurtosis kurtosis-0.244
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha353900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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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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8. Citations (2)

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9. Files and Curves (10)