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5vf3

Bacteriophage T4 isometric capsid

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid vertex protein gp24

OrganismNot specified

UniProt P19896

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 1560 Major capsid protein × 720 （P04535） Small outer capsid protein × 660 （P03715） Highly immunogenic outer capsid protein × 60 （P18056） Highly immunogenic outer capsid protein × 60 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 26 Major capsid protein × 12 （P04535） Small outer capsid protein × 11 （P03715） Highly immunogenic outer capsid protein × 1 （P18056） Highly immunogenic outer capsid protein × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 130 Major capsid protein × 60 （P04535） Small outer capsid protein × 55 （P03715） Highly immunogenic outer capsid protein × 5 （P18056） Highly immunogenic outer capsid protein × 5 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 156 Major capsid protein × 72 （P04535） Small outer capsid protein × 66 （P03715） Highly immunogenic outer capsid protein × 6 （P18056） Highly immunogenic outer capsid protein × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 26 Major capsid protein × 12 （P04535） Small outer capsid protein × 11 （P03715） Highly immunogenic outer capsid protein × 1 （P18056） Highly immunogenic outer capsid protein × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1yue

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5vf3 5vf3 5vf3 5vf3 5vf3 7vrt 7vrt 7vrt 7vs5 7vs5 7vs5 8gmo

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CAPSP_BPT4
Isoform —
PDB entities 1
Chains and sequence ranges Author chain a； PDBConstruct 1–417； UniProt 11–427

Major capsid protein

OrganismNot specified

UniProt P04535

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 1560 Capsid vertex protein gp24 × 60 （P19896） Small outer capsid protein × 660 （P03715） Highly immunogenic outer capsid protein × 60 （P18056） Highly immunogenic outer capsid protein × 60 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 26 Capsid vertex protein gp24 × 1 （P19896） Small outer capsid protein × 11 （P03715） Highly immunogenic outer capsid protein × 1 （P18056） Highly immunogenic outer capsid protein × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 130 Capsid vertex protein gp24 × 5 （P19896） Small outer capsid protein × 55 （P03715） Highly immunogenic outer capsid protein × 5 （P18056） Highly immunogenic outer capsid protein × 5 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 156 Capsid vertex protein gp24 × 6 （P19896） Small outer capsid protein × 66 （P03715） Highly immunogenic outer capsid protein × 6 （P18056） Highly immunogenic outer capsid protein × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 26 Capsid vertex protein gp24 × 1 （P19896） Small outer capsid protein × 11 （P03715） Highly immunogenic outer capsid protein × 1 （P18056） Highly immunogenic outer capsid protein × 1 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
5vf3 5vf3 5vf3 5vf3 5vf3 6uzc 7vrt 7vrt 7vrt 7vs5 7vs5 7vs5

19 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CAPSH_BPT4
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–456； UniProt 66–521 Author chain B； PDBConstruct 1–456； UniProt 66–521 Author chain C； PDBConstruct 1–456； UniProt 66–521 Author chain D； PDBConstruct 1–456； UniProt 66–521 Author chain E； PDBConstruct 1–456； UniProt 66–521 Author chain F； PDBConstruct 1–456； UniProt 66–521 Author chain G； PDBConstruct 1–456； UniProt 66–521 Author chain H； PDBConstruct 1–456； UniProt 66–521 Author chain I； PDBConstruct 1–456； UniProt 66–521 Author chain J； PDBConstruct 1–456； UniProt 66–521 Author chain K； PDBConstruct 1–456； UniProt 66–521 Author chain L； PDBConstruct 1–456； UniProt 66–521

Small outer capsid protein

OrganismNot specified

UniProt P03715

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 1560 Capsid vertex protein gp24 × 60 （P19896） Major capsid protein × 720 （P04535） Highly immunogenic outer capsid protein × 60 （P18056） Highly immunogenic outer capsid protein × 60 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 26 Capsid vertex protein gp24 × 1 （P19896） Major capsid protein × 12 （P04535） Highly immunogenic outer capsid protein × 1 （P18056） Highly immunogenic outer capsid protein × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 130 Capsid vertex protein gp24 × 5 （P19896） Major capsid protein × 60 （P04535） Highly immunogenic outer capsid protein × 5 （P18056） Highly immunogenic outer capsid protein × 5 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 156 Capsid vertex protein gp24 × 6 （P19896） Major capsid protein × 72 （P04535） Highly immunogenic outer capsid protein × 6 （P18056） Highly immunogenic outer capsid protein × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 26 Capsid vertex protein gp24 × 1 （P19896） Major capsid protein × 12 （P04535） Highly immunogenic outer capsid protein × 1 （P18056） Highly immunogenic outer capsid protein × 1 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
5vf3 5vf3 5vf3 5vf3 5vf3 7vs5 7vs5 7vs5

8 assemblies

View Construct and Data Evidence
UniProt name VSOC_BPT4
Isoform —
PDB entities 3
Chains and sequence ranges Author chain O； PDBConstruct 1–80； UniProt 1–80 Author chain P； PDBConstruct 1–80； UniProt 1–80 Author chain Q； PDBConstruct 1–80； UniProt 1–80 Author chain R； PDBConstruct 1–80； UniProt 1–80 Author chain S； PDBConstruct 1–80； UniProt 1–80 Author chain T； PDBConstruct 1–80； UniProt 1–80 Author chain U； PDBConstruct 1–80； UniProt 1–80 Author chain V； PDBConstruct 1–80； UniProt 1–80 Author chain W； PDBConstruct 1–80； UniProt 1–80 Author chain X； PDBConstruct 1–80； UniProt 1–80 Author chain Y； PDBConstruct 1–80； UniProt 1–80

Highly immunogenic outer capsid protein

OrganismNot specified

UniProt P18056

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 1560 Capsid vertex protein gp24 × 60 （P19896） Major capsid protein × 720 （P04535） Small outer capsid protein × 660 （P03715） Highly immunogenic outer capsid protein × 60 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 26 Capsid vertex protein gp24 × 1 （P19896） Major capsid protein × 12 （P04535） Small outer capsid protein × 11 （P03715） Highly immunogenic outer capsid protein × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 130 Capsid vertex protein gp24 × 5 （P19896） Major capsid protein × 60 （P04535） Small outer capsid protein × 55 （P03715） Highly immunogenic outer capsid protein × 5 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 156 Capsid vertex protein gp24 × 6 （P19896） Major capsid protein × 72 （P04535） Small outer capsid protein × 66 （P03715） Highly immunogenic outer capsid protein × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 26 Capsid vertex protein gp24 × 1 （P19896） Major capsid protein × 12 （P04535） Small outer capsid protein × 11 （P03715） Highly immunogenic outer capsid protein × 1 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
5vf3 5vf3 5vf3 5vf3 5vf3

5 assemblies

View Construct and Data Evidence
UniProt name HOC_BPT4
Isoform —
PDB entities 4
Chains and sequence ranges Author chain Z； PDBConstruct 1–376； UniProt 1–376

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_id5vf3
Deposition date deposition_date2017-04-06
Structure title titleBacteriophage T4 isometric capsid
Keywords keywords;Bacteriophage T4, isometric head, virus capsid assembly, triangulation numbers, size-determining mutations, capsid stabilization, capsid decoration proteins, VIRUS ;; VIRUS
Experimental Method methodELECTRON MICROSCOPY
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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.

5vf3__assembly_1__model_1

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

Download this curve (.dat)

5vf3__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.

5vf3__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)406.00 Å
Total Rg406.00 Å
Atom count3095040
Residues407760
Excluded volume54933000 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5vf3__assembly_1__model_1 1560-meric （1560） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5vf3__assembly_2__model_1 26-meric （26） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 5vf3__assembly_3__model_1 130-meric （130） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 5vf3__assembly_4__model_1 156-meric （156） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 5vf3__assembly_5__model_1 26-meric （26） 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) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id5vf3O00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3P00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3Q00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3R00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3S00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3T00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3U00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3V00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3W00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3X00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
Domain ID domain_id5vf3Y00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily20 — Small outer capsid protein Soc
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7. Citations (1)