4zor

The structure of the S37P MS2 viral capsid assembly.

Method: X-RAY DIFFRACTION Dmax: 112.3 Å Quality: GOOD

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

Coat protein

Enterobacteria 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 homooligomer Homooligomer Protein × 60 PDB declaration: 60-meric(60) Consistent with protein copy count Chain A; UniProt 2–130 Chain B; UniProt 2–130 Chain C; UniProt 2–130 Chain D; UniProt 2–130 Chain E; UniProt 2–130 Mutation:S38P PO4 PHOSPHATE ION × 48 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;299 K;1.8M lithium sulphate, 100mM TRIS, pH 7.55, 20% glycerol (cryo) Resolution 2.20 Å R-free 0.242

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 208 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 2–130 Author chain B; PDBConstruct 1–129; UniProt 2–130 Author chain C; PDBConstruct 1–129; UniProt 2–130 Author chain D; PDBConstruct 1–129; UniProt 2–130 Author chain E; 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 4zor

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zor
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4zor
Deposition date deposition_date2015-05-06
Structure title titleThe structure of the S37P MS2 viral capsid assembly.
Keywords keywordsCapsid, VIRUS LIKE PARTICLE, VIRUS; VIRUS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.89
Radius of gyration Rg (electron density) rg_electron37.21
Forward intensity I(0) i074560000.00
Molecular weight molecular_weight67658.0 kDa
Excluded volume excluded_volume84422 ų
Envelope volume envelope_volume144960 ų
Hydration-shell volume shell_volume33672 ų
Envelope diameter envelope_diameter111.7
Shell Rg shell_rg42.57
Envelope Rg envelope_rg35.24
Shape Rg shape_rg37.17
Total Rg total_rg37.80
Total atoms total_atoms9379
Residues n_residues630
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 dmax112.3
Rg (real space) rg_real37.74
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real7.4560e+07
I(0) uncertainty (real space) i0_real_error1.3220e+06
Rg (reciprocal space) rg_reciprocal37.84
I(0) (reciprocal space) i0_reciprocal74570000.0000
Solution quality estimate total_estimate0.8864
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.1
Skewness Skewness skewness0.044
Kurtosis Kurtosis kurtosis-0.738
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6342000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.995; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.538

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd4zora_
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_idd4zorb_
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_idd4zorc_
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_idd4zord_
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_idd4zore_
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 (5 domains)

Domain ID domain_id4zorA00
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_id4zorB00
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_id4zorC00
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_id4zorD00
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_id4zorE00
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)