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1rb8

The phiX174 DNA binding protein J in two different capsid environments.

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

Capsid protein

OrganismNot specified

UniProt P08767

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 Major spike protein × 60 （P31281） Small core protein × 60 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 60 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360 Consistent with all polymers
2 Protein–DNA Heteromer Protein 3 DNA 1 Major spike protein × 1 （P31281） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 Consistent with all polymers
3 Protein–DNA Heteromer Protein 15 DNA 5 Major spike protein × 5 （P31281） Small core protein × 5 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 5 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30 Consistent with all polymers
4 Protein–DNA Heteromer Protein 18 DNA 6 Major spike protein × 6 （P31281） Small core protein × 6 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 6 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36 Consistent with all polymers
5 Protein–DNA Heteromer Protein 3 DNA 1 Major spike protein × 1 （P31281） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 Consistent with all polymers
6 Protein–DNA Heteromer Protein 60 DNA 20 Major spike protein × 20 （P31281） Small core protein × 20 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 20 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 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
1m06 1m06 1m06 1m06 1m06 1m06 1m0f 1m0f 1m0f 1m0f 1m0f 1rb8

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VGF_BPAL3
Isoform —
PDB entities 1
Chains and sequence ranges Author chain F； PDBConstruct 1–431； UniProt 1–431

Major spike protein

OrganismNot specified

UniProt P31281

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 Capsid protein × 60 （P08767） Small core protein × 60 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 60 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360 Consistent with all polymers
2 Protein–DNA Heteromer Protein 3 DNA 1 Capsid protein × 1 （P08767） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 Consistent with all polymers
3 Protein–DNA Heteromer Protein 15 DNA 5 Capsid protein × 5 （P08767） Small core protein × 5 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 5 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30 Consistent with all polymers
4 Protein–DNA Heteromer Protein 18 DNA 6 Capsid protein × 6 （P08767） Small core protein × 6 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 6 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36 Consistent with all polymers
5 Protein–DNA Heteromer Protein 3 DNA 1 Capsid protein × 1 （P08767） Small core protein × 1 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 Consistent with all polymers
6 Protein–DNA Heteromer Protein 60 DNA 20 Capsid protein × 20 （P08767） Small core protein × 20 （P69592） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 20 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 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
1m06 1m06 1m06 1m06 1m06 1m06 1m0f 1m0f 1m0f 1m0f 1m0f 1rb8

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VGG_BPAL3
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 1–187； UniProt 1–187

Small core protein

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 Capsid protein × 60 （P08767） Major spike protein × 60 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 60 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 360 Consistent with all polymers
2 Protein–DNA Heteromer Protein 3 DNA 1 Capsid protein × 1 （P08767） Major spike protein × 1 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 Consistent with all polymers
3 Protein–DNA Heteromer Protein 15 DNA 5 Capsid protein × 5 （P08767） Major spike protein × 5 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 5 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 30 Consistent with all polymers
4 Protein–DNA Heteromer Protein 18 DNA 6 Capsid protein × 6 （P08767） Major spike protein × 6 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 6 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 36 Consistent with all polymers
5 Protein–DNA Heteromer Protein 3 DNA 1 Capsid protein × 1 （P08767） Major spike protein × 1 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 6 Consistent with all polymers
6 Protein–DNA Heteromer Protein 60 DNA 20 Capsid protein × 20 （P08767） Major spike protein × 20 （P31281） ;DNA (5'-D(P*CP*AP*AP*A)-3') ; × 20 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 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
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 3
Chains and sequence ranges Author chain J； PDBConstruct 1–37； UniProt 1–37

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_id1rb8
Deposition date deposition_date2003-11-03
Structure title titleThe phiX174 DNA binding protein J in two different capsid environments.
Keywords keywords;bacteriophage alpha3, bacteriophage phiX174, bacteriophage alpha3 chimera, alpha3, phiX174, three-dimentional structure, virion, Microviridae, 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.

1rb8__assembly_1__model_1

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

Download this curve (.dat)

1rb8__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.

1rb8__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)126.10 Å
Total Rg126.20 Å
Atom count306720
Residues38340
Excluded volume5397500 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1rb8__assembly_1__model_1 240-MERIC （240） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1rb8__assembly_2__model_1 tetrameric （4） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 1rb8__assembly_3__model_1 eicosameric （20） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 1rb8__assembly_4__model_1 24-meric （24） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 1rb8__assembly_5__model_1 tetrameric （4） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6 1 1rb8__assembly_6__model_1 80-meric （80） 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_idd1rb8f_
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_idd1rb8g_
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_id1rb8F00
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_id1rb8G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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7. Citations (4)