1u1y

Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position

Method: X-RAY DIFFRACTION Dmax: 87.9 Å Quality: EXCELLENT

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 120 PDB declaration: 300-MERIC(300) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Not recorded 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3' × 120 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 coat protein in 1.25% or 1.5% PEG 8K, sodium phosphate buffer., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.85 Å R-free 0.196
2 Protein–RNA Homooligomer Protein × 3 RNA 2 PDB declaration: pentameric(5) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Not recorded 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3' × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 coat protein in 1.25% or 1.5% PEG 8K, sodium phosphate buffer., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.85 Å R-free 0.196
3 Protein–RNA Homooligomer Protein × 15 RNA 10 PDB declaration: 25-meric(25) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Not recorded 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3' × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 coat protein in 1.25% or 1.5% PEG 8K, sodium phosphate buffer., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.85 Å R-free 0.196
4 Protein–RNA Homooligomer Protein × 18 RNA 12 PDB declaration: 30-meric(30) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Not recorded 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3' × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 coat protein in 1.25% or 1.5% PEG 8K, sodium phosphate buffer., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.85 Å R-free 0.196
5 Protein–RNA Homooligomer Protein × 3 RNA 2 PDB declaration: pentameric(5) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Not recorded 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3' × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 coat protein in 1.25% or 1.5% PEG 8K, sodium phosphate buffer., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.85 Å R-free 0.196
6 Protein–RNA Homooligomer Protein × 30 RNA 20 PDB declaration: 50-meric(50) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Not recorded 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3' × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;303 K;MS2 coat protein in 1.25% or 1.5% PEG 8K, sodium phosphate buffer., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.85 Å R-free 0.196

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 1u1y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1u1y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1u1y
Deposition date deposition_date2004-07-16
Structure title titleCrystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position
Keywords keywordsComplex (Capsid protein-RNA hairpin), Hairpin, Capsid, Levivirus, Icosahedral virus, Virus-RNA COMPLEX; Virus/RNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.66
Radius of gyration Rg (electron density) rg_electron26.81
Forward intensity I(0) i060058300.00
Molecular weight molecular_weight51773.0 kDa
Excluded volume excluded_volume61373 ų
Envelope volume envelope_volume93470 ų
Hydration-shell volume shell_volume29437 ų
Envelope diameter envelope_diameter91.9
Shell Rg shell_rg33.62
Envelope Rg envelope_rg26.54
Shape Rg shape_rg26.81
Total Rg total_rg27.56
Total atoms total_atoms3596
Residues n_residues418
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 dmax87.9
Rg (real space) rg_real27.52
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real6.0060e+07
I(0) uncertainty (real space) i0_real_error9.2120e+05
Rg (reciprocal space) rg_reciprocal27.56
I(0) (reciprocal space) i0_reciprocal60060000.0000
Solution quality estimate total_estimate0.9005
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.0
Skewness Skewness skewness0.136
Kurtosis Kurtosis kurtosis-0.500
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4189000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1u1ya_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.85 — RNA bacteriophage capsid protein
Superfamily Superfamily superfamilyd.85.1 — RNA bacteriophage capsid protein
Family Family familyd.85.1.1 — RNA bacteriophage capsid protein
Domain ID domain_idd1u1yb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.85 — RNA bacteriophage capsid protein
Superfamily Superfamily superfamilyd.85.1 — RNA bacteriophage capsid protein
Family Family familyd.85.1.1 — RNA bacteriophage capsid protein
Domain ID domain_idd1u1yc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.85 — RNA bacteriophage capsid protein
Superfamily Superfamily superfamilyd.85.1 — RNA bacteriophage capsid protein
Family Family familyd.85.1.1 — RNA bacteriophage capsid protein

CATH v4.4 (3 domains)

Domain ID domain_id1u1yA00
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_id1u1yB00
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_id1u1yC00
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)