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1pgl

BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT

Method: X-RAY DIFFRACTION Dmax: 97.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT

OrganismNot specified

UniProt P23009

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 × 120 RNA 60 PDB declaration: 180-MERIC（180） Consistent with all polymer counts Chain 1； UniProt 821–1005 Chain 2； UniProt 447–816 Not recorded 5'-R(*AP*GP*UP*CP*UP*C)-3' × 60 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00 Resolution 2.80 Å
2 Protein–RNA Homooligomer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain 1； UniProt 821–1005 Chain 2； UniProt 447–816 Not recorded 5'-R(*AP*GP*UP*CP*UP*C)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00 Resolution 2.80 Å
3 Protein–RNA Homooligomer Protein × 10 RNA 5 PDB declaration: pentadecameric（15） Consistent with all polymer counts Chain 1； UniProt 821–1005 Chain 2； UniProt 447–816 Not recorded 5'-R(*AP*GP*UP*CP*UP*C)-3' × 5 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00 Resolution 2.80 Å
4 Protein–RNA Homooligomer Protein × 12 RNA 6 PDB declaration: octadecameric（18） Consistent with all polymer counts Chain 1； UniProt 821–1005 Chain 2； UniProt 447–816 Not recorded 5'-R(*AP*GP*UP*CP*UP*C)-3' × 6 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00 Resolution 2.80 Å
5 Protein–RNA Homooligomer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain 1； UniProt 821–1005 Chain 2； UniProt 447–816 Not recorded 5'-R(*AP*GP*UP*CP*UP*C)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00 Resolution 2.80 Å
6 Protein–RNA Homooligomer Protein × 60 RNA 30 PDB declaration: 90-meric（90） Consistent with all polymer counts Chain 1； UniProt 821–1005 Chain 2； UniProt 447–816 Not recorded 5'-R(*AP*GP*UP*CP*UP*C)-3' × 30 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00 Resolution 2.80 Å

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.

Other PDB Difference from Current Entry 1PGL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BMV PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION Deposited 1989-10-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 120 PDB declaration: complete icosahedral assembly
Chain 1 821–1018（198 aa）
Chain 2 447–820（374 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BMV PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION Deposited 1989-10-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain 1 821–1018（198 aa）
Chain 2 447–820（374 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BMV PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION Deposited 1989-10-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Homooligomer；Protein × 10 PDB declaration: pentadecameric
Chain 1 821–1018（198 aa）
Chain 2 447–820（374 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BMV PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION Deposited 1989-10-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein–RNA Homooligomer；Protein × 12 PDB declaration: octadecameric
Chain 1 821–1018（198 aa）
Chain 2 447–820（374 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BMV PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION Deposited 1989-10-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 5 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain 1 821–1018（198 aa）
Chain 2 447–820（374 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BMV PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION Deposited 1989-10-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 6 Protein–RNA Homooligomer；Protein × 60 PDB declaration: 90-meric
Chain 1 821–1018（198 aa）
Chain 2 447–820（374 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 120 PDB declaration: 120-MERIC
Chain 1 821–1005（185 aa）
Chain 2 466–816（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain 1 821–1005（185 aa）
Chain 2 466–816（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain 1 821–1005（185 aa）
Chain 2 466–816（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain 1 821–1005（185 aa）
Chain 2 466–816（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain 1 821–1005（185 aa）
Chain 2 466–816（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Resolution 2.90 Å
1PGW BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT Deposited 2003-05-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain 1 821–1005（185 aa）
Chain 2 466–816（351 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Resolution 2.90 Å

2 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGNM_BPMV
Isoform —
PDB entities 2, 3
Chains and sequence ranges Author chain 1； PDBConstruct 1–185； UniProt 821–1005 Author chain 2； PDBConstruct 1–370； UniProt 447–816

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 1pgl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1pgl
Deposition date deposition_date2003-05-28
Structure title titleBEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT
Keywords keywordsCOMOVIRUS, VIRUS, VIRAL COAT PROTEIN, BEAN POD MOTTLE VIRUS (BPMV), Icosahedral virus, Virus-RNA COMPLEX; Virus/RNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.39 Å
Radius of gyration Rg (electron density) rg_electron26.80 Å
Forward intensity I(0) i066849000.00
Molecular weight molecular_weight63209.0 kDa
Excluded volume excluded_volume78773 ų
Envelope volume envelope_volume95943 ų
Hydration-shell volume shell_volume30615 ų
Envelope diameter envelope_diameter104.3 Å
Shell Rg shell_rg33.27 Å
Envelope Rg envelope_rg27.47 Å
Shape Rg shape_rg26.81 Å
Total Rg total_rg27.44 Å
Total atoms total_atoms4425
Residues n_residues561
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax97.7 Å
Rg (real space) rg_real27.45 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real6.6850e+07
I(0) uncertainty (real space) i0_real_error1.0680e+06
Rg (reciprocal space) rg_reciprocal27.44 Å
I(0) (reciprocal space) i0_reciprocal66850000.0000
Solution quality estimate total_estimate0.8538
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3 Å
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.247
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14030000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.729; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.964
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1pgl11
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.2 — Comoviridae-like VP
Domain ID domain_idd1pgl21
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.2 — Comoviridae-like VP
Domain ID domain_idd1pgl22
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.2 — Comoviridae-like VP

CATH v4.4 (2 domains)

Domain ID domain_id1pgl100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1pgl200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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8. Citations (2)

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9. Files and Curves (10)