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2bpa

ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS

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

PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)

Enterobacteria phage phiX174

UniProt P03641

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 180 DNA 60 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 60 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P69592） water × 240 Consistent with all polymers
2 Protein–DNA Heteromer Protein 3 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） water × 4 Consistent with all polymers
3 Protein–DNA Heteromer Protein 15 DNA 5 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 5 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P69592） water × 20 Consistent with all polymers
4 Protein–DNA Heteromer Protein 18 DNA 6 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 6 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P69592） water × 24 Consistent with all polymers
5 Protein–DNA Heteromer Protein 3 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1kvp 1kvp

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
1kvp 1kvp 1kvp

3 assemblies

Heteromeric or nucleic-acid complex
1al0 1al0 1al0 1al0 1al0 1al0 1cd3 1cd3 1cd3 1cd3 1cd3 1cd3

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VGF_BPPHX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain 1； PDBConstruct 1–426； UniProt 1–426

PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)

Enterobacteria phage phiX174

UniProt P03643

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 180 DNA 60 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 60 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P69592） water × 240 Consistent with all polymers
2 Protein–DNA Heteromer Protein 3 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） water × 4 Consistent with all polymers
3 Protein–DNA Heteromer Protein 15 DNA 5 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 5 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P69592） water × 20 Consistent with all polymers
4 Protein–DNA Heteromer Protein 18 DNA 6 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 6 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P69592） water × 24 Consistent with all polymers
5 Protein–DNA Heteromer Protein 3 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P69592） water × 4 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
1al0 1al0 1al0 1al0 1al0 1al0 1cd3 1cd3 1cd3 1cd3 1cd3 1cd3

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VGG_BPPHX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain 2； PDBConstruct 1–175； UniProt 1–175

PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)

Enterobacteria phage phiX174

UniProt P69592

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 180 DNA 60 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 60 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 60 （P03643） water × 240 Consistent with all polymers
2 Protein–DNA Heteromer Protein 3 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） water × 4 Consistent with all polymers
3 Protein–DNA Heteromer Protein 15 DNA 5 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 5 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 5 （P03643） water × 20 Consistent with all polymers
4 Protein–DNA Heteromer Protein 18 DNA 6 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 6 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 6 （P03643） water × 24 Consistent with all polymers
5 Protein–DNA Heteromer Protein 3 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*C)-3') ; × 1 PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03641） PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174) × 1 （P03643） water × 4 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
1rb8 1rb8 1rb8 1rb8 1rb8 1rb8 2bpa 2bpa 2bpa 2bpa 2bpa 9k3m

12 assemblies

View Construct and Data Evidence
UniProt name VGJ_BPPHX
Isoform —
PDB entities 4
Chains and sequence ranges Author chain 3； PDBConstruct 1–37； UniProt 2–38

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_id2bpa
Deposition date deposition_date1991-12-03
Structure title titleATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS
Keywords keywordsPROTEIN-DNA COMPLEX, SINGLE STRAND, Icosahedral virus, Virus-DNA COMPLEX; Virus/DNA
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.

2bpa__assembly_1__model_1

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

Download this curve (.dat)

2bpa__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.

2bpa__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)125.90 Å
Total Rg125.90 Å
Atom count307200
Residues38520
Excluded volume5430400 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2bpa__assembly_1__model_1 240-MERIC （240） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2bpa__assembly_2__model_1 tetrameric （4） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 2bpa__assembly_3__model_1 eicosameric （20） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 2bpa__assembly_4__model_1 24-meric （24） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 2bpa__assembly_5__model_1 tetrameric （4） 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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2bpa1_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.5 — ssDNA viruses
Family Family familyb.121.5.1 — Microviridae-like VP
Domain ID domain_idd2bpa2_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.5 — ssDNA viruses
Family Family familyb.121.5.1 — Microviridae-like VP

CATH v4.4 (2 domains)

Domain ID domain_id2bpa100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology169 — Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1
Homologous superfamily homologous superfamily10 — Microviridae F protein
Domain ID domain_id2bpa200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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7. Citations (6)