5msf

MS2 PROTEIN CAPSID/RNA COMPLEX

Method: X-RAY DIFFRACTION Dmax: 87.2 Å Quality: EXCELLENT

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

MS2 PROTEIN CAPSID

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 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Not recorded 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3' × 120 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;300 K;PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA. Resolution 2.80 Å R-free 0.197
2 Protein–RNA Homooligomer Protein × 3 RNA 2 PDB declaration: pentameric(5) Consistent with all polymer counts Chain A; UniProt 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Not recorded 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3' × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;300 K;PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA. Resolution 2.80 Å R-free 0.197
3 Protein–RNA Homooligomer Protein × 15 RNA 10 PDB declaration: 25-meric(25) Consistent with all polymer counts Chain A; UniProt 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Not recorded 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3' × 10 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;300 K;PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA. Resolution 2.80 Å R-free 0.197
4 Protein–RNA Homooligomer Protein × 18 RNA 12 PDB declaration: 30-meric(30) Consistent with all polymer counts Chain A; UniProt 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Not recorded 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3' × 12 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;300 K;PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA. Resolution 2.80 Å R-free 0.197
5 Protein–RNA Homooligomer Protein × 3 RNA 2 PDB declaration: pentameric(5) Consistent with all polymer counts Chain A; UniProt 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Not recorded 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3' × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;300 K;PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA. Resolution 2.80 Å R-free 0.197
6 Protein–RNA Homooligomer Protein × 30 RNA 20 PDB declaration: 50-meric(50) Consistent with all polymer counts Chain A; UniProt 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Not recorded 5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3' × 20 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.4;300 K;PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA. Resolution 2.80 Å R-free 0.197

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 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 5msf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5msf
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5msf
Deposition date deposition_date1998-05-15
Structure title titleMS2 PROTEIN CAPSID/RNA COMPLEX
Keywords keywordsCAPSID PROTEIN MS2-RNA APTAMER COMPLEX, RNA-PROTEIN COMPLEX, RNA STEM LOOP, BACTERIOPHAGE MS2, 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_guinier27.68
Radius of gyration Rg (electron density) rg_electron26.77
Forward intensity I(0) i061326100.00
Molecular weight molecular_weight52169.0 kDa
Excluded volume excluded_volume61755 ų
Envelope volume envelope_volume93444 ų
Hydration-shell volume shell_volume29464 ų
Envelope diameter envelope_diameter91.6
Shell Rg shell_rg33.67
Envelope Rg envelope_rg26.51
Shape Rg shape_rg26.76
Total Rg total_rg27.55
Total atoms total_atoms3623
Residues n_residues421
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 dmax87.2
Rg (real space) rg_real27.53
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real6.1330e+07
I(0) uncertainty (real space) i0_real_error9.1840e+05
Rg (reciprocal space) rg_reciprocal27.58
I(0) (reciprocal space) i0_reciprocal61330000.0000
Solution quality estimate total_estimate0.9018
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.7
Skewness Skewness skewness0.130
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4200000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.973

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_idd5msfa_
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_idd5msfb_
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_idd5msfc_
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_id5msfA00
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_id5msfB00
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_id5msfC00
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 (5)

9. Files and Curves (10)