9q1d

MS2 bacteriophage coat protein with waters modeled

Method: ELECTRON MICROSCOPY Dmax: 91.6 Å Quality: GOOD

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

Capsid protein

Escherichia phage MS2

UniProt P03612

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 × 180 PDB declaration: 180-meric(180) Consistent with protein copy count Chain A; UniProt 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5;100 mM Tris-HCl [pH 8.5], 80 mM KCl, 10 mM MgCl2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.75 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.

43 other PDB entries and 208 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAPSD_BPMS2
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–129; UniProt 2–130 Author chain B; PDBConstruct 1–129; UniProt 2–130 Author chain C; PDBConstruct 1–129; UniProt 2–130

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 9q1d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9q1d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9q1d
Deposition date deposition_date2025-08-13
Structure title titleMS2 bacteriophage coat protein with waters modeled
Keywords keywordsBacteriophage, VLP, MS2, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier26.90
Radius of gyration Rg (electron density) rg_electron26.43
Forward intensity I(0) i029336100.00
Molecular weight molecular_weight41189.0 kDa
Excluded volume excluded_volume51506 ų
Envelope volume envelope_volume68850 ų
Hydration-shell volume shell_volume23192 ų
Envelope diameter envelope_diameter93.5
Shell Rg shell_rg31.57
Envelope Rg envelope_rg27.08
Shape Rg shape_rg26.46
Total Rg total_rg26.99
Total atoms total_atoms2895
Residues n_residues387
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax91.6
Rg (real space) rg_real27.11
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real2.9340e+07
I(0) uncertainty (real space) i0_real_error4.5490e+05
Rg (reciprocal space) rg_reciprocal27.04
I(0) (reciprocal space) i0_reciprocal29330000.0000
Solution quality estimate total_estimate0.8424
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4
Skewness Skewness skewness0.533
Kurtosis Kurtosis kurtosis-0.244
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3726000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.805; Smooth: 0.848

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)