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1al0

PROCAPSID OF BACTERIOPHAGE PHIX174

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

SCAFFOLDING PROTEIN GPD

OrganismNot specified

UniProt P69486

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 420 CAPSID PROTEIN GPF × 60 （P03641） SPIKE PROTEIN GPG × 60 （P03643） SCAFFOLDING PROTEIN GPB × 60 （P03633） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 7 CAPSID PROTEIN GPF × 1 （P03641） SPIKE PROTEIN GPG × 1 （P03643） SCAFFOLDING PROTEIN GPB × 1 （P03633） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 35 CAPSID PROTEIN GPF × 5 （P03641） SPIKE PROTEIN GPG × 5 （P03643） SCAFFOLDING PROTEIN GPB × 5 （P03633） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 42 CAPSID PROTEIN GPF × 6 （P03641） SPIKE PROTEIN GPG × 6 （P03643） SCAFFOLDING PROTEIN GPB × 6 （P03633） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 7 CAPSID PROTEIN GPF × 1 （P03641） SPIKE PROTEIN GPG × 1 （P03643） SCAFFOLDING PROTEIN GPB × 1 （P03633） Consistent with protein count
6 Protein heterocomplex Heteromer Protein 280 CAPSID PROTEIN GPF × 40 （P03641） SPIKE PROTEIN GPG × 40 （P03643） SCAFFOLDING PROTEIN GPB × 40 （P03633） Consistent with protein count

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

12 assemblies

View Construct and Data Evidence
UniProt name VGD_BPPHX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain 1； PDBConstruct 2–152； UniProt 1–151 Author chain 2； PDBConstruct 2–152； UniProt 1–151 Author chain 3； PDBConstruct 2–152； UniProt 1–151 Author chain 4； PDBConstruct 2–152； UniProt 1–151

CAPSID PROTEIN GPF

OrganismNot specified

UniProt P03641

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 420 SCAFFOLDING PROTEIN GPD × 240 （P69486） SPIKE PROTEIN GPG × 60 （P03643） SCAFFOLDING PROTEIN GPB × 60 （P03633） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 7 SCAFFOLDING PROTEIN GPD × 4 （P69486） SPIKE PROTEIN GPG × 1 （P03643） SCAFFOLDING PROTEIN GPB × 1 （P03633） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 35 SCAFFOLDING PROTEIN GPD × 20 （P69486） SPIKE PROTEIN GPG × 5 （P03643） SCAFFOLDING PROTEIN GPB × 5 （P03633） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 42 SCAFFOLDING PROTEIN GPD × 24 （P69486） SPIKE PROTEIN GPG × 6 （P03643） SCAFFOLDING PROTEIN GPB × 6 （P03633） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 7 SCAFFOLDING PROTEIN GPD × 4 （P69486） SPIKE PROTEIN GPG × 1 （P03643） SCAFFOLDING PROTEIN GPB × 1 （P03633） Consistent with protein count
6 Protein heterocomplex Heteromer Protein 280 SCAFFOLDING PROTEIN GPD × 160 （P69486） SPIKE PROTEIN GPG × 40 （P03643） SCAFFOLDING PROTEIN GPB × 40 （P03633） Consistent with protein count

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 F； PDBConstruct 1–426； UniProt 1–426

SPIKE PROTEIN GPG

OrganismNot specified

UniProt P03643

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 420 SCAFFOLDING PROTEIN GPD × 240 （P69486） CAPSID PROTEIN GPF × 60 （P03641） SCAFFOLDING PROTEIN GPB × 60 （P03633） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 7 SCAFFOLDING PROTEIN GPD × 4 （P69486） CAPSID PROTEIN GPF × 1 （P03641） SCAFFOLDING PROTEIN GPB × 1 （P03633） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 35 SCAFFOLDING PROTEIN GPD × 20 （P69486） CAPSID PROTEIN GPF × 5 （P03641） SCAFFOLDING PROTEIN GPB × 5 （P03633） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 42 SCAFFOLDING PROTEIN GPD × 24 （P69486） CAPSID PROTEIN GPF × 6 （P03641） SCAFFOLDING PROTEIN GPB × 6 （P03633） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 7 SCAFFOLDING PROTEIN GPD × 4 （P69486） CAPSID PROTEIN GPF × 1 （P03641） SCAFFOLDING PROTEIN GPB × 1 （P03633） Consistent with protein count
6 Protein heterocomplex Heteromer Protein 280 SCAFFOLDING PROTEIN GPD × 160 （P69486） CAPSID PROTEIN GPF × 40 （P03641） SCAFFOLDING PROTEIN GPB × 40 （P03633） Consistent with protein count

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 G； PDBConstruct 1–175； UniProt 1–175

SCAFFOLDING PROTEIN GPB

OrganismNot specified

UniProt P03633

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 420 SCAFFOLDING PROTEIN GPD × 240 （P69486） CAPSID PROTEIN GPF × 60 （P03641） SPIKE PROTEIN GPG × 60 （P03643） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 7 SCAFFOLDING PROTEIN GPD × 4 （P69486） CAPSID PROTEIN GPF × 1 （P03641） SPIKE PROTEIN GPG × 1 （P03643） Consistent with protein count
3 Protein heterocomplex Heteromer Protein 35 SCAFFOLDING PROTEIN GPD × 20 （P69486） CAPSID PROTEIN GPF × 5 （P03641） SPIKE PROTEIN GPG × 5 （P03643） Consistent with protein count
4 Protein heterocomplex Heteromer Protein 42 SCAFFOLDING PROTEIN GPD × 24 （P69486） CAPSID PROTEIN GPF × 6 （P03641） SPIKE PROTEIN GPG × 6 （P03643） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 7 SCAFFOLDING PROTEIN GPD × 4 （P69486） CAPSID PROTEIN GPF × 1 （P03641） SPIKE PROTEIN GPG × 1 （P03643） Consistent with protein count
6 Protein heterocomplex Heteromer Protein 280 SCAFFOLDING PROTEIN GPD × 160 （P69486） CAPSID PROTEIN GPF × 40 （P03641） SPIKE PROTEIN GPG × 40 （P03643） Consistent with protein count

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

12 assemblies

View Construct and Data Evidence
UniProt name VGB_BPPHX
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–120； UniProt 1–120

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_id1al0
Deposition date deposition_date1997-06-06
Structure title titlePROCAPSID OF BACTERIOPHAGE PHIX174
Keywords keywordsCOMPLEX (VIRUS CAPSID PROTEINS), BACTERIOPHAGE, PROCAPSID, SCAFFOLDING PROTEIN, CHAPERONE, Icosahedral virus, 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.

1al0__assembly_1__model_1

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

Download this curve (.dat)

1al0__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.

1al0__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)139.80 Å
Total Rg140.00 Å
Atom count571260
Residues72240
Excluded volume10149000 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1al0__assembly_1__model_1 complete icosahedral assembly （420） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1al0__assembly_2__model_1 heptameric （7） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 1al0__assembly_3__model_1 35-meric （35） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 1al0__assembly_4__model_1 42-meric （42） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 1al0__assembly_5__model_1 heptameric （7） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6 1 1al0__assembly_6__model_1 280-meric （280） 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) 13 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1al01_
Class classa — All alpha proteins
Fold Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
Domain ID domain_idd1al02_
Class classa — All alpha proteins
Fold Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
Domain ID domain_idd1al03_
Class classa — All alpha proteins
Fold Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
Domain ID domain_idd1al04_
Class classa — All alpha proteins
Fold Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
Domain ID domain_idd1al0f_
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_idd1al0g_
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 (7 domains)

Domain ID domain_id1al0100
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily10 — Scaffold protein D
Domain ID domain_id1al0200
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily10 — Scaffold protein D
Domain ID domain_id1al0300
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily10 — Scaffold protein D
Domain ID domain_id1al0400
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily10 — Scaffold protein D
Domain ID domain_id1al0B00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology1260 — Scaffolding protein gpD of bacteriophage procapsid fold
Homologous superfamily homologous superfamily10 — Scaffolding protein gpD of bacteriophage procapsid
Domain ID domain_id1al0F00
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_id1al0G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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7. Citations (6)