2b2d

RNA stemloop operator from bacteriophage QBETA complexed with an N87S,E89K mutant MS2 capsid

Method: X-RAY DIFFRACTION Dmax: 90.2 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 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:N87S, E89K 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-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 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.90 Å R-free 0.203
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:N87S, E89K 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-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 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.90 Å R-free 0.203
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:N87S, E89K 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-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 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.90 Å R-free 0.203
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:N87S, E89K 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-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 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.90 Å R-free 0.203
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:N87S, E89K 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-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 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.90 Å R-free 0.203
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 Mutation:N87S, E89K 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-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 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 2.90 Å R-free 0.203

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 2b2d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2b2d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2b2d
Deposition date deposition_date2005-09-19
Structure title titleRNA stemloop operator from bacteriophage QBETA complexed with an N87S,E89K mutant MS2 capsid
Keywords keywordscapsid, complex (capsid protein - RNA hairpin) hairpin, levivirus, VIRUS/VIRAL, protein/RNA, VIRUS-VIRAL PROTEIN-RNA COMPLEX; VIRUS/VIRAL PROTEIN/RNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.33
Radius of gyration Rg (electron density) rg_electron26.06
Forward intensity I(0) i038347300.00
Molecular weight molecular_weight44960.0 kDa
Excluded volume excluded_volume55127 ų
Envelope volume envelope_volume72461 ų
Hydration-shell volume shell_volume24576 ų
Envelope diameter envelope_diameter93.9
Shell Rg shell_rg31.61
Envelope Rg envelope_rg26.64
Shape Rg shape_rg26.09
Total Rg total_rg26.57
Total atoms total_atoms3144
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 dmax90.2
Rg (real space) rg_real26.49
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real3.8350e+07
I(0) uncertainty (real space) i0_real_error5.9160e+05
Rg (reciprocal space) rg_reciprocal26.44
I(0) (reciprocal space) i0_reciprocal38350000.0000
Solution quality estimate total_estimate0.8502
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.538
Kurtosis Kurtosis kurtosis-0.144
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3973000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.945

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_idd2b2da_
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_idd2b2db_
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_idd2b2dc_
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_id2b2dA00
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_id2b2dB00
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_id2b2dC00
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)