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2qqp

Crystal Structure of Authentic Providence Virus

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

p81

OrganismNot specified

UniProt Q80IX5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Homooligomer Protein 480 RNA 60 ;RNA (5'-R(*UP*UP*UP*U)-3') ; × 60 CALCIUM ION × 120 water × 240 Consistent with all polymers
2 Protein–RNA Homooligomer Protein 8 RNA 1 ;RNA (5'-R(*UP*UP*UP*U)-3') ; × 1 CALCIUM ION × 2 water × 4 Consistent with all polymers
3 Protein–RNA Homooligomer Protein 40 RNA 5 ;RNA (5'-R(*UP*UP*UP*U)-3') ; × 5 CALCIUM ION × 10 water × 20 Consistent with all polymers
4 Protein–RNA Homooligomer Protein 48 RNA 6 ;RNA (5'-R(*UP*UP*UP*U)-3') ; × 6 CALCIUM ION × 12 water × 24 Consistent with all polymers
5 Protein–RNA Homooligomer Protein 8 RNA 1 ;RNA (5'-R(*UP*UP*UP*U)-3') ; × 1 CALCIUM ION × 2 water × 4 Consistent with all polymers
6 Protein–RNA Homooligomer Protein 240 RNA 30 ;RNA (5'-R(*UP*UP*UP*U)-3') ; × 30 CALCIUM ION × 60 water × 120 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
2qqp 2qqp 2qqp 2qqp 2qqp 2qqp

6 assemblies

View Construct and Data Evidence
UniProt name Q80IX5_PRVFL
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–556； UniProt 124–679 Author chain C； PDBConstruct 1–556； UniProt 124–679 Author chain E； PDBConstruct 1–556； UniProt 124–679 Author chain G； PDBConstruct 1–556； UniProt 124–679 Author chain B； PDBConstruct 1–75； UniProt 680–754 Author chain D； PDBConstruct 1–75； UniProt 680–754 Author chain F； PDBConstruct 1–75； UniProt 680–754 Author chain H； PDBConstruct 1–75； UniProt 680–754

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_id2qqp
Deposition date deposition_date2007-07-26
Structure title titleCrystal Structure of Authentic Providence Virus
Keywords keywords;virus, capsid, coat protein, protein-RNA complex, beta barrel, Ig-like domain, tetravirus, tetraviridae, icosahedral virus, quasiequivalence, auto-catalytic cleavage, auto proteolysis ;; VIRUS
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.

2qqp__assembly_1__model_1

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

Download this curve (.dat)

2qqp__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 1011 1012 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2qqp__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)164.30 Å
Total Rg164.30 Å
Atom count997680
Residues131400
Excluded volume17661000 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2qqp__assembly_1__model_1 540-MERIC （540） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2qqp__assembly_2__model_1 nonameric （9） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 2qqp__assembly_3__model_1 45-meric （45） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 2qqp__assembly_4__model_1 54-meric （54） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 2qqp__assembly_5__model_1 nonameric （9） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6 1 2qqp__assembly_6__model_1 270-meric （270） 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 (5)

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6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id2qqpA01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology350 — V-type ATP synthase subunit C fold
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2qqpA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2qqpA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4260 —
Domain ID domain_id2qqpC01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology350 — V-type ATP synthase subunit C fold
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2qqpC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2qqpC03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4260 —
Domain ID domain_id2qqpD00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily650 —
Domain ID domain_id2qqpE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1690 — V-type ATP synthase subunit C fold
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2qqpE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2qqpE03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4260 —
Domain ID domain_id2qqpG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1690 — V-type ATP synthase subunit C fold
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2qqpG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2qqpG03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4260 —
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7. Citations (2)