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1pgl

BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT

Method: X-RAY DIFFRACTION
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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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Homooligomer Protein 120 RNA 60 5'-R(*AP*GP*UP*CP*UP*C)-3' × 60 water × 180 Consistent with all polymers
2 Protein–RNA Homooligomer Protein 2 RNA 1 5'-R(*AP*GP*UP*CP*UP*C)-3' × 1 water × 3 Consistent with all polymers
3 Protein–RNA Homooligomer Protein 10 RNA 5 5'-R(*AP*GP*UP*CP*UP*C)-3' × 5 water × 15 Consistent with all polymers
4 Protein–RNA Homooligomer Protein 12 RNA 6 5'-R(*AP*GP*UP*CP*UP*C)-3' × 6 water × 18 Consistent with all polymers
5 Protein–RNA Homooligomer Protein 2 RNA 1 5'-R(*AP*GP*UP*CP*UP*C)-3' × 1 water × 3 Consistent with all polymers
6 Protein–RNA Homooligomer Protein 60 RNA 30 5'-R(*AP*GP*UP*CP*UP*C)-3' × 30 water × 90 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1pgw 1pgw

2 assemblies

Homotetramer

None

Other homooligomers
1pgw 1pgw 1pgw 1pgw

4 assemblies

Heteromeric or nucleic-acid complex
1bmv 1bmv 1bmv 1bmv 1bmv 1bmv 1pgl 1pgl 1pgl 1pgl 1pgl 1pgl

12 assemblies

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.

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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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1pgl__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1pgl__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 1011 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1pgl__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）0.00 Å
Rg (electron density)124.30 Å
Total Rg124.20 Å
Atom count265500
Residues33660
Excluded volume4726400 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1pgl__assembly_1__model_1 180-MERIC （180） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1pgl__assembly_2__model_1 trimeric （3） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 1pgl__assembly_3__model_1 pentadecameric （15） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 1pgl__assembly_4__model_1 octadecameric （18） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 1pgl__assembly_5__model_1 trimeric （3） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6 1 1pgl__assembly_6__model_1 90-meric （90） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. 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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7. Citations (2)