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3dpr

Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3

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

Protein VP1

OrganismNot specified

UniProt P04936

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 300 LDL-receptor class A 3 × 60 （P98155） LAURIC ACID × 60 CALCIUM ION × 60 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 LDL-receptor class A 3 × 1 （P98155） LAURIC ACID × 1 CALCIUM ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 25 LDL-receptor class A 3 × 5 （P98155） LAURIC ACID × 5 CALCIUM ION × 5 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 30 LDL-receptor class A 3 × 6 （P98155） LAURIC ACID × 6 CALCIUM ION × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 5 LDL-receptor class A 3 × 1 （P98155） LAURIC ACID × 1 CALCIUM ION × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 300 LDL-receptor class A 3 × 60 （P98155） LAURIC ACID × 60 CALCIUM ION × 60 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1cqq 2hrv 2hrv 2xya 5fx5 5fx6 6ffn 6ffs

8 assemblies

Homodimer
7ara

1 assemblies

Homotetramer
1fpn 1fpn 3vdd 3vdd

4 assemblies

Other homooligomers
1fpn 1fpn 1fpn 1fpn 3tn9 3tn9 3tn9 3tn9 3tn9 3tn9 3vdd 3vdd

22 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
1a3r 1v9u 1v9u 1v9u 1v9u 1v9u 1v9u 3dpr 3dpr 3dpr 3dpr 3dpr

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name POLG_HRV2
Isoform —
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain A； PDBConstruct 1–289； UniProt 568–856 Author chain B； PDBConstruct 1–261； UniProt 70–330 Author chain C； PDBConstruct 1–237； UniProt 331–567 Author chain D； PDBConstruct 1–68； UniProt 2–69

LDL-receptor class A 3

Homo sapiens

UniProt P98155

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 300 Protein VP1 × 60 （P04936） Protein VP2 × 60 （P04936） Protein VP3 × 60 （P04936） Protein VP4 × 60 （P04936） LAURIC ACID × 60 CALCIUM ION × 60 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Protein VP1 × 1 （P04936） Protein VP2 × 1 （P04936） Protein VP3 × 1 （P04936） Protein VP4 × 1 （P04936） LAURIC ACID × 1 CALCIUM ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 25 Protein VP1 × 5 （P04936） Protein VP2 × 5 （P04936） Protein VP3 × 5 （P04936） Protein VP4 × 5 （P04936） LAURIC ACID × 5 CALCIUM ION × 5 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 30 Protein VP1 × 6 （P04936） Protein VP2 × 6 （P04936） Protein VP3 × 6 （P04936） Protein VP4 × 6 （P04936） LAURIC ACID × 6 CALCIUM ION × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 5 Protein VP1 × 1 （P04936） Protein VP2 × 1 （P04936） Protein VP3 × 1 （P04936） Protein VP4 × 1 （P04936） LAURIC ACID × 1 CALCIUM ION × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 300 Protein VP1 × 60 （P04936） Protein VP2 × 60 （P04936） Protein VP3 × 60 （P04936） Protein VP4 × 60 （P04936） LAURIC ACID × 60 CALCIUM ION × 60 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6byv

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1v9u 1v9u 1v9u 1v9u 1v9u 1v9u 3dpr 3dpr 3dpr 3dpr 3dpr 3dpr

35 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VLDLR_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–39； UniProt 113–151

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_id3dpr
Deposition date deposition_date2008-07-09
Structure title titleHuman rhinovirus 2 bound to a concatamer of the VLDL receptor module V3
Keywords keywords;HUMAN RHINOVIRUS, VLDL-RECEPTOR, VIRUS-PROTEIN COMPLEX, ICOSAHEDRAL VIRUS, ATP-binding, Capsid protein, Covalent protein-RNA linkage, Cytoplasmic vesicle, Helicase, Host-virus interaction, Hydrolase, Lipoprotein, Membrane, Myristate, Nucleotide-binding, Nucleotidyltransferase, Phosphoprotein, Protease, RNA replication, RNA-binding, RNA-directed RNA polymerase, Thiol protease, Transferase, Virion, Cholesterol metabolism, Coated pit, EGF-like domain, Endocytosis, Glycoprotein, Lipid metabolism, Lipid transport, Receptor, Steroid metabolism, Transmembrane, Transport, VLDL, VIRUS ;; 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.

3dpr__assembly_1__model_1

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

Download this curve (.dat)

3dpr__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.

3dpr__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)133.70 Å
Total Rg133.80 Å
Atom count387000
Residues49200
Excluded volume6843900 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3dpr__assembly_1__model_1 300-MERIC （300） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3dpr__assembly_2__model_1 pentameric （5） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 3dpr__assembly_3__model_1 25-meric （25） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 3dpr__assembly_4__model_1 30-meric （30） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 3dpr__assembly_5__model_1 pentameric （5） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6 1 3dpr__assembly_6__model_1 300-meric （300） 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 (7)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3dprA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3dprB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3dprC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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7. Citations (1)