2bq5

MS2 (N87AE89K mutant) - RNA hairpin complex

Method: X-RAY DIFFRACTION Dmax: 89.2 Å Quality: GOOD

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

COAT PROTEIN

BACTERIOPHAGE 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 Mutation:YES ;5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' ; × 120 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.91 Å R-free 0.298
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 Mutation:YES ;5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' ; × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.91 Å R-free 0.298
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 Mutation:YES ;5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' ; × 10 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.91 Å R-free 0.298
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 Mutation:YES ;5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' ; × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.91 Å R-free 0.298
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 Mutation:YES ;5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' ; × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.91 Å R-free 0.298
6 Protein–RNA Homooligomer Protein × 90 RNA 60 PDB declaration: 150-meric(150) Consistent with all polymer counts Chain A; UniProt 1–129 Chain B; UniProt 1–129 Chain C; UniProt 1–129 Mutation:YES ;5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' ; × 60 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.91 Å R-free 0.298

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 1
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 2bq5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bq5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bq5
Deposition date deposition_date2005-04-27
Structure title titleMS2 (N87AE89K mutant) - RNA hairpin complex
Keywords keywords;VIRUS/RNA, CAPSID, COMPLEX (CAPSID PROTEIN-RNA HAIRPIN), HAIRPIN, LEVIVIRUS, VIRUS/VIRAL PROTEIN/RNA, VIRUS COAT PROTEIN, 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_guinier27.53
Radius of gyration Rg (electron density) rg_electron26.91
Forward intensity I(0) i060924500.00
Molecular weight molecular_weight52551.0 kDa
Excluded volume excluded_volume62303 ų
Envelope volume envelope_volume85330 ų
Hydration-shell volume shell_volume27482 ų
Envelope diameter envelope_diameter93.5
Shell Rg shell_rg33.01
Envelope Rg envelope_rg27.02
Shape Rg shape_rg26.92
Total Rg total_rg27.49
Total atoms total_atoms3646
Residues n_residues423
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 dmax89.2
Rg (real space) rg_real27.57
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real6.0920e+07
I(0) uncertainty (real space) i0_real_error9.0250e+05
Rg (reciprocal space) rg_reciprocal27.56
I(0) (reciprocal space) i0_reciprocal60920000.0000
Solution quality estimate total_estimate0.8614
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.8
Skewness Skewness skewness0.374
Kurtosis Kurtosis kurtosis-0.388
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4112000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.552

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id2bq5A00
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_id2bq5B00
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_id2bq5C00
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)