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1ddl

DESMODIUM YELLOW MOTTLE TYMOVIRUS

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DESMODIUM YELLOW MOTTLE VIRUS

OrganismNot specified

UniProt O89511

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Homooligomer Protein 180 RNA 120 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') ; × 60 ;RNA (5'-R(P*UP*U)-3') ; × 60 water × 240 Consistent with all polymers
2 Protein–RNA Homooligomer Protein 3 RNA 2 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') ; × 1 ;RNA (5'-R(P*UP*U)-3') ; × 1 water × 4 Consistent with all polymers
3 Protein–RNA Homooligomer Protein 15 RNA 10 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') ; × 5 ;RNA (5'-R(P*UP*U)-3') ; × 5 water × 20 Consistent with all polymers
4 Protein–RNA Homooligomer Protein 18 RNA 12 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') ; × 6 ;RNA (5'-R(P*UP*U)-3') ; × 6 water × 24 Consistent with all polymers
5 Protein–RNA Homooligomer Protein 3 RNA 2 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') ; × 1 ;RNA (5'-R(P*UP*U)-3') ; × 1 water × 4 Consistent with all polymers
6 Protein–RNA Homooligomer Protein 15 RNA 10 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') ; × 5 ;RNA (5'-R(P*UP*U)-3') ; × 5 water × 20 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ddl 1ddl 1ddl 1ddl 1ddl 1ddl

6 assemblies

View Construct and Data Evidence
UniProt name O89511_9VIRU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–188； UniProt 1–188 Author chain B； PDBConstruct 1–188； UniProt 1–188 Author chain C； PDBConstruct 1–188； UniProt 1–188

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_id1ddl
Deposition date deposition_date1999-11-10
Structure title titleDESMODIUM YELLOW MOTTLE TYMOVIRUS
Keywords keywordsPLANT VIRUS, DYMV, CAPSID PROTEIN, COAT PROTEIN, TYMOVIRUSES, WATER STRUCTURE, RNA, 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.

1ddl__assembly_1__model_1

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

Download this curve (.dat)

1ddl__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.

1ddl__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)129.10 Å
Total Rg129.10 Å
Atom count258420
Residues33600
Excluded volume4613700 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ddl__assembly_1__model_1 300-MERIC （300） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1ddl__assembly_2__model_1 pentameric （5） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 1ddl__assembly_3__model_1 25-meric （25） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 1ddl__assembly_4__model_1 30-meric （30） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 1ddl__assembly_5__model_1 pentameric （5） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6 1 1ddl__assembly_6__model_1 25-meric （25） 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) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1ddla_
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.121.4.6 — Tymoviridae-like VP
Domain ID domain_idd1ddlb_
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.121.4.6 — Tymoviridae-like VP
Domain ID domain_idd1ddlc_
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.121.4.6 — Tymoviridae-like VP

CATH v4.4 (3 domains)

Domain ID domain_id1ddlA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1ddlB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1ddlC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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7. Citations (1)