1zse

RNA stemloop from bacteriophage Qbeta complexed with an N87S mutant MS2 Capsid

Method: X-RAY DIFFRACTION Dmax: 91.7 Å Quality: GOOD

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

Coat protein

Enterobacterio 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–RNA Homooligomer Protein × 180 RNA 60 PDB declaration: 240-MERIC(240) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Mutation:N87S RNA HAIRPIN × 60 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.00 Å R-free 0.232
2 Protein–RNA Homooligomer Protein × 3 RNA 1 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Mutation:N87S RNA HAIRPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.00 Å R-free 0.232
3 Protein–RNA Homooligomer Protein × 15 RNA 5 PDB declaration: eicosameric(20) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Mutation:N87S RNA HAIRPIN × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.00 Å R-free 0.232
4 Protein–RNA Homooligomer Protein × 18 RNA 6 PDB declaration: 24-meric(24) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Mutation:N87S RNA HAIRPIN × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.00 Å R-free 0.232
5 Protein–RNA Homooligomer Protein × 3 RNA 1 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Mutation:N87S RNA HAIRPIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.00 Å R-free 0.232
6 Protein–RNA Homooligomer Protein × 30 RNA 10 PDB declaration: 40-meric(40) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Mutation:N87S RNA HAIRPIN × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 COATPROTEIN IN 1.25% OR 1.5% PEG 8K, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.00 Å R-free 0.232

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 203 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COAT_BPMS2
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–129; UniProt 1–129 Author chain B; PDBConstruct 1–129; UniProt 1–129 Author chain C; PDBConstruct 1–129; UniProt 1–129

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 1zse

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zse
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zse
Deposition date deposition_date2005-05-24
Structure title titleRNA stemloop from bacteriophage Qbeta complexed with an N87S mutant MS2 Capsid
Keywords keywordscapsid, complex (capsid protein - rna hairpin), hairpin, levivirus, virus/viral protein/rna, RNA-VIRUS-VIRAL PROTEIN COMPLEX; RNA/VIRUS/VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.02
Radius of gyration Rg (electron density) rg_electron25.89
Forward intensity I(0) i038709000.00
Molecular weight molecular_weight44950.0 kDa
Excluded volume excluded_volume55017 ų
Envelope volume envelope_volume72412 ų
Hydration-shell volume shell_volume24771 ų
Envelope diameter envelope_diameter93.8
Shell Rg shell_rg31.24
Envelope Rg envelope_rg26.51
Shape Rg shape_rg25.93
Total Rg total_rg26.38
Total atoms total_atoms3143
Residues n_residues399
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 dmax91.7
Rg (real space) rg_real26.19
Rg uncertainty (real space) rg_real_error0.88
I(0) (real space) i0_real3.8710e+07
I(0) uncertainty (real space) i0_real_error6.5230e+05
Rg (reciprocal space) rg_reciprocal26.14
I(0) (reciprocal space) i0_reciprocal38710000.0000
Solution quality estimate total_estimate0.8329
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.569
Kurtosis Kurtosis kurtosis-0.063
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4270000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.652; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id1zseA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology380 — MS2 Viral Coat Protein
Homologous superfamily homologous superfamily10 — MS2 Viral Coat Protein
Domain ID domain_id1zseB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology380 — MS2 Viral Coat Protein
Homologous superfamily homologous superfamily10 — MS2 Viral Coat Protein
Domain ID domain_id1zseC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology380 — MS2 Viral Coat Protein
Homologous superfamily homologous superfamily10 — MS2 Viral Coat Protein

8. Citations (1)

9. Files and Curves (10)