Bacteriophage Capsid Morphogenesis, Genome Packaging, and Tail Assembly

A reusable module capturing bacteriophage virion morphogenesis (`GO:0019068`) across tailed dsDNA phages (Caudoviricetes), tailless icosahedral phages, internal-membrane phages (Tectiviridae), and segmented dsRNA cystoviruses. The core tailed-phage assembly pathway comprises procapsid assembly on a portal vertex (`GO:0019069`, `GO:0046798`), proteolytic or conformational procapsid maturation and expansion (`GO:0046797`, `GO:0019082`), ATP-driven genome packaging (`GO:0019073`) via a `VariantSetDescriptor` distinguishing 5'-cos (`GO:0098037`), headful pac/non-pac (`GO:0098006`), terminal-protein-primed phi29 packaging, PRD1 vertex ATPase P9 packaging, and phi6 hexameric P4 ssRNA packaging, followed by head completion/decoration (`GO:0098021`), independent tail and tail fiber assembly (`GO:0098003`, `GO:0098004`), and head-tail joining (`GO:0098005`). Also captures satellite phage capsid hijacking (such as P4 Sid redirecting helper P2 gpN procapsids into small T=4 heads).

MODULE:phage_capsid_packaging_and_tail_assemblyCOMPLETECONCRETEBiological Processmodules/phage_capsid_packaging_and_tail_assembly.yaml
virion assemblyGO:0019068 viral capsid assemblyGO:0019069 viral DNA genome packagingGO:0019073 viral tail assemblyGO:0098003
PMID:28893988
Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses.
High-resolution cryo-EM structure of the T4 capsid defines the HK97-fold major capsid protein gp23*, vertex protein gp24*, and outer capsid decoration proteins Hoc and Soc.
The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers.
PMID:26144253
Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.
The dodecameric T4 gp20 portal complex nucleates prohead assembly, docks the gp17 terminase motor for DNA packaging, and connects to the neck and tail after packaging completion.
The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging.
PMID:4920094
Analysis of T4 phage proteins. I. Conversion of precursor proteins into lower molecular weight peptides during normal capsid formation.
Proteolytic cleavage of capsid and internal scaffold precursors by the T4 prohead protease gp21 drives procapsid maturation and expansion prior to DNA packaging.
Pulse-chase experiments combined with differential extraction indicated that conversion of P23 into A-protein and alteration of the protein coded by gene 22 (P22) appeared to be vital steps in formation of normal capsids.
PMID:8892827
Characterization of the helper proteins for the assembly of tail fibers of coliphages T4 and lambda.
Dedicated phage-encoded tail fiber assembly chaperones (such as T4 gp38 and gp57A, and lambda Tfa) catalyze folding and trimerization of distal tail fibers without remaining in the mature virion or acting as minor fiber components.
Assembly of tail fibers of coliphage T4 requires the action of helper proteins. In the absence of one of these, protein 38 (p38), p37, constituting the distal part of the long tail fiber, fails to oligomerize.
file:projects/PHAGES.md
Bacteriophage Genome & Module Curation Plan
Defines the capsid morphogenesis, genome packaging variant set, tail assembly, and satellite capsid redirection architecture.
`GO:0098006` headful packaging (T4, P22, P1) vs. `GO:0098037` 5'-extended `cos` packaging (λ, P2) vs. terminal-protein (`gp3`)/pRNA-primed packaging (φ29) vs. vertex ATPase packaging without a canonical terminase (PRD1, φ6).

Curated for the Bacteriophage Genome & Module Curation project. Notice that in cellular location slots (`locations`), `GO:0110165` (cellular anatomical entity) descendants such as `GO:0030430` (host cell cytoplasm, where intracellular virion assembly and packaging take place) are used because `GO:0044423` (virion component) and its descendants (`GO:0019030` icosahedral viral capsid, `GO:0098021` viral capsid, decoration, `GO:0098015` virus tail) sit directly under `GO:0005575` (cellular_component) rather than `GO:0110165`, while protein-complex terms (`GO:0046798` viral portal complex, `GO:0043493` viral terminase complex) are placed in `protein_complex` when needed, satisfying GO branch constraints.

10Nodes
3Parts
1Variant Sets
6Variants
10Annotons
0Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:phage_capsid_packaging_and_tail_assembly deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

0 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (10 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
major_capsid_and_decoration_shell ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
portal_vertex_nucleation ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
baseplate_and_tail_tube_sheath_morphogenesis ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
tail_fiber_chaperone_and_whisker_assembly ANY_PARTICIPANT
Gene 		protein folding chaperone
GO:0044183 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
headful_terminase_and_end_protection ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
cos_terminase_packaging ANY_WITH_FUNCTION
Gene 		DNA translocase activity
GO:0015616 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
phi29_tp_packaging_motor ANY_WITH_FUNCTION
Gene 		DNA translocase activity
GO:0015616 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
prd1_p9_vertex_packaging_atpase ANY_WITH_FUNCTION
Gene 		ATP hydrolysis activity
GO:0016887 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
cystovirus_p4_rna_packaging_motor ANY_PARTICIPANT
Gene 		nucleoside-triphosphatase activity
GO:0017111 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
coat_operator_or_ssdna_coupled_encapsidation ANY_WITH_FUNCTION
Gene 		structural constituent of virion
GO:0039660 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.

Gene-review completeness (8/10 grounded genes reviewed)

8 complete review(s) · 5 with deep research · 2 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
19 P13333 ✓ ✓ ✓
2 P15076 ✓ ✓ ✓
20 P13334 ✓ ✓ ✓
38 P03739 ✓ ✓ ✓
A P03708 ✓ ✓ ✗
cp P03612 ✓ ✓ ✗
gp23 P04535 ✓ ✓ ✓
16 (Bacillus phage phi29) P11014 ✗ — —
IX (Enterobacteria phage PRD1) P27381 ✗ — —
P4 P11125 ✓ ✓ ✗

Details

Context
VirusesNCBITaxon:10239 BacteriaNCBITaxon:2
Bacteriophage Capsid Morphogenesis, Genome Packaging, and Tail AssemblyBiological Processphage_capsid_packaging_and_tail_assembly
virion assemblyGO:0019068 viral capsid assemblyGO:0019069 viral DNA genome packagingGO:0019073 viral tail assemblyGO:0098003
Context
VirusesNCBITaxon:10239 BacteriaNCBITaxon:2
Part 1: major capsid shell assembly, maturation, and outer capsid decoration
Major capsid shell assembly, procapsid maturation, and decorationBiological Processmajor_capsid_shell_assembly

Every bacteriophage assembles a proteinaceous capsid or coat shell (`GO:0019069`) from major capsid subunits (e.g. T4 gp23, lambda gpE, T7 gp10A/B, phiX174 gpF, MS2 coat, PRD1 P3, phi6 P1) assisted where applicable by internal or external scaffolding proteins (`GO:0046806`, e.g. T4 gp22, lambda Nu3, T7 gp9, phiX174 gpB/gpD), prohead maturation proteases (`GO:0046797`, T4 gp21, lambda gpC), and outer capsid decoration clamps (`GO:0098021`, T4 Soc/Hoc, lambda gpD).

Annotons

Major capsid shell assembly and outer capsid decoration
major_capsid_and_decoration_shell
Participant: Any With Function: gp23 (Bacteriophage T4)
Gene Product:
gp23 (Bacteriophage T4)UniProtKB:P04535
Required Function:
structural constituent of virionGO:0039660
Major capsid coat proteins (T4 gp23, lambda gpE, T7 gp10, P22 gp5, phiX174 gpF, MS2 coat, PRD1 P3) and outer capsid decoration clamp proteins (T4 Soc/Hoc, lambda gpD) that form and reinforce the mature virion capsid.

Function

structural constituent of virionGO:0039660

Processes

viral capsid assemblyGO:0019069

Locations

host cell cytoplasmGO:0030430

Assembles the procapsid or coat lattice and matures into the infectious capsid shell.

PMID:28893988
T4 gp23* forms the hexameric capsid lattice reinforced by Soc and Hoc decoration proteins.
The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers.
Part 2: dodecameric portal vertex nucleation and procapsid maturation in tailed phages (optional)
Dodecameric portal vertex procapsid nucleation and maturationBiological Processportal_vertex_procapsid_nucleation

In tailed dsDNA phages (Caudoviricetes), a dodecameric portal ring (e.g. T4 gp20, lambda gpB, T7 gp8, P22 gp1, phi29 gp10) forms a unique 12-fold vertex (`GO:0046798`) that nucleates procapsid assembly, coordinates scaffold/protease-mediated procapsid maturation (`GO:0046797`), docks the packaging motor, and serves as the attachment site for neck and tail completion proteins.

Annotons

Dodecameric portal vertex nucleation of procapsid assembly and maturation
portal_vertex_nucleation
Participant: Any With Function: 20 (Bacteriophage T4)
Gene Product:
20 (Bacteriophage T4)UniProtKB:P13334
Required Function:
structural constituent of virionGO:0039660
Dodecameric portal vertex protein (T4 gp20, lambda gpB, T7 gp8, P22 gp1, phi29 gp10) that forms the unique 12-fold vertex for procapsid initiation, procapsid maturation, DNA translocation, and tail attachment.

Function

structural constituent of virionGO:0039660

Processes

viral capsid assemblyGO:0019069 viral procapsid maturationGO:0046797 viral DNA genome packagingGO:0019073

Locations

host cell cytoplasmGO:0030430

Forms the conduit vertex that nucleates prohead assembly and docks the packaging motor.

PMID:26144253
Dodecameric T4 gp20 forms the portal vertex for prohead assembly and DNA packaging.
The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging.
Part 3: independent tail and tail fiber assembly and head-tail joining (optional)
Tail morphogenesis, chaperone-assisted fiber assembly, and head-tail joiningBiological Processtail_assembly_and_head_tail_joining

In myoviruses and siphoviruses, the tail (baseplate/tip, tube, and sheath) and tail fibers assemble along independent morphogenetic pathways assisted by dedicated assembly chaperones (e.g. T4 gp51 baseplate hub assembly catalyst, gp26/gp28/gp48/gp54 baseplate-tube initiators, gp38 and gp57A tail fiber chaperones, and wac fibritin whiskers) before joining to the DNA-filled head via neck/connector proteins (`GO:0098005`).

Annotons

Baseplate, tail tube, and tail sheath assembly
baseplate_and_tail_tube_sheath_morphogenesis
Participant: Any With Function: 19 (Bacteriophage T4)
Gene Product:
19 (Bacteriophage T4)UniProtKB:P13333
Required Function:
structural constituent of virionGO:0039660
Baseplate hub and wedge structural subunits (T4 gp5, gp6, gp7, gp8, gp9, gp10, gp11, gp25, gp26, gp27, gp28, gp29, gp48, gp53, gp54), catalytic hub assembly protein (gp51), tail tube (gp19), and tail sheath (gp18).

Function

structural constituent of virionGO:0039660

Processes

viral tail assemblyGO:0098003 viral head-tail joiningGO:0098005

Locations

host cell cytoplasmGO:0030430

Constructs the contractile or non-contractile tail complex and joins it to the packaged capsid portal/neck vertex.

Chaperone-catalyzed tail fiber folding and attachment
tail_fiber_chaperone_and_whisker_assembly
Participant: Any Participant: 38 (Bacteriophage T4)
Gene Product:
38 (Bacteriophage T4)UniProtKB:P03739
Non-structural tail fiber molecular chaperones (T4 gp38, gp57A) and collar/whisker attachment helpers (T4 wac fibritin) that mediate trimerization and attachment of long and short tail fibers (gp34, gp35, gp36, gp37, gp12).

Function

protein folding chaperoneGO:0044183

Processes

virus tail fiber assemblyGO:0098004

Locations

host cell cytoplasmGO:0030430

Directs folding, trimerization, and virion attachment of phage tail fibers.

PMID:8892827
Helper proteins such as T4 gp38 catalyze the folding and assembly of phage tail fibers.
Assembly of tail fibers of coliphage T4 requires the action of helper proteins. In the absence of one of these, protein 38 (p38), p37, constituting the distal part of the long tail fiber, fails to oligomerize.
Variant set: Bacteriophage genome packaging mechanism by packaging substrate recognition and translocation motor (Exactly One)

Bacteriophages package their replicated genomes into preformed procapsids using distinct recognition and motor strategies.

Headful dsDNA concatemer packaging (T4/P22/P1/P2-type)Biological Processheadful_dna_packaging

Large terminase ATPase/nuclease (e.g. T4 gp17, P22 gp2) and small terminase DNA-recognition subunit (T4 gp16, P22 gp3) translocate concatemeric dsDNA (`GO:0015616`) until the capsid head is >100% full, making a terminal cleavage that yields circularly permuted, terminally redundant chromosomes (`GO:0098006`), protected against host RecBCD exonuclease by DNA end-protection proteins (such as T4 gp2).

Annotons

Headful terminase DNA translocation and genome end protection
headful_terminase_and_end_protection
Participant: Any With Function: 2 (Bacteriophage T4)
Gene Product:
2 (Bacteriophage T4)UniProtKB:P15076
Required Function:
structural constituent of virionGO:0039660
Headful packaging machinery (T4 terminase gp16/gp17) and packaged DNA-end protection protein (T4 gp2) that caps newly cleaved concatemer ends to prevent host RecBCD degradation after ejection.

Function

structural constituent of virionGO:0039660

Processes

viral DNA genome packaging, headfulGO:0098006

Locations

host cell cytoplasmGO:0030430

Packages concatemeric dsDNA by a headful gauge mechanism and protects the packaged linear DNA termini.

Cohesive-end (cos) sequence-specific dsDNA packaging (lambda/P2/P4-type)Biological Processcos_site_dna_packaging

Terminase complex (e.g. lambda Nu1 small subunit + A large subunit) recognizes specific cos sites on concatemeric DNA and introduces staggered nicks generating 5'-extended (`GO:0098037`) or 3'-extended (`GO:0098036`) cohesive ends at unit-length boundaries (`GO:0098035`).

Annotons

Sequence-specific cos terminase DNA packaging
cos_terminase_packaging
Participant: Any With Function: A (Escherichia phage lambda)
Gene Product:
A (Escherichia phage lambda)UniProtKB:P03708
Required Function:
DNA translocase activityGO:0015616
Cohesive-end terminase holoenzyme (lambda Nu1/A, P2 M/P) that cleaves cos sites and translocates unit-length dsDNA into the procapsid.

Function

DNA translocase activityGO:0015616

Processes

viral DNA genome packaging, 5' extended cos packagingGO:0098037

Locations

host cell cytoplasmGO:0030430

Introduces site-specific staggered nicks at cos sequences and packages unit-length genomes.

Terminal-protein (gp3) and pRNA-assisted dsDNA packaging (phi29-type)Biological Processterminal_protein_pRNA_packaging

Unit-length dsDNA covalently linked at its 5' ends to terminal protein gp3 is translocated into the prohead by the gp16 packaging ATPase anchored on a prohead RNA (pRNA) ring at the gp10 connector.

Annotons

Terminal-protein-guided dsDNA packaging ATPase
phi29_tp_packaging_motor
Participant: Any With Function: 16 (Bacillus phage phi29)
Gene Product:
16 (Bacillus phage phi29)UniProtKB:P11014
Required Function:
DNA translocase activityGO:0015616
phi29 packaging ATPase gp16 acting with connector gp10, pRNA, and terminal protein gp3 to package unit-length TP-DNA.

Function

DNA translocase activityGO:0015616

Processes

viral DNA genome packagingGO:0019073

Locations

host cell cytoplasmGO:0030430

Translocates covalent terminal-protein-dsDNA complexes into the procapsid.

Internal-membrane vertex ATPase dsDNA packaging (PRD1 P9-type)Biological Processinternal_membrane_vertex_atpase_packaging

Tailless internal-membrane dsDNA tectiviruses (PRD1) package unit-length linear TP-dsDNA into preformed procapsids through a unique membrane-associated vertex (P20/P22/P6) powered by the virion-incorporated packaging ATPase P9 (`GO:0016887`, `GO:0019073`) without a canonical terminase nuclease or prohead RNA.

Annotons

Vertex-mounted ATPase linear dsDNA packaging motor
prd1_p9_vertex_packaging_atpase
Participant: Any With Function: IX (Enterobacteria phage PRD1)
Gene Product:
IX (Enterobacteria phage PRD1)UniProtKB:P27381
Required Function:
ATP hydrolysis activityGO:0016887
Tectivirus PRD1 packaging ATPase P9 and unique vertex complex proteins (P6, P20, P22) that translocate linear terminal-protein-linked dsDNA across the internal viral membrane into the procapsid.

Function

ATP hydrolysis activityGO:0016887

Processes

viral DNA genome packagingGO:0019073

Locations

host cell cytoplasmGO:0030430

Hydrolyzes ATP at the unique membrane vertex to package linear TP-dsDNA into the procapsid.

Sequential segmented (+)ssRNA procapsid packaging (phi6 P4-type)Biological Processcystovirus_segmented_ssrna_packaging

Enveloped dsRNA cystoviruses (phi6) package single-stranded (+)RNA precursors (s+, m+, l+) in strict sequential order through vertex-mounted hexameric P4 NTPase motors into the P1/P2/P4/P7 procapsid prior to intra-capsid minus-strand dsRNA synthesis.

Annotons

Hexameric P4 NTPase sequential (+)ssRNA packaging
cystovirus_p4_rna_packaging_motor
Participant: Any Participant: P4 (Pseudomonas phage phi6)
Gene Product:
P4 (Pseudomonas phage phi6)UniProtKB:P11125
Hexameric NTP-driven RNA translocation motor P4 mounted at procapsid vertices of Pseudomonas phage phi6.

Function

nucleoside-triphosphatase activityGO:0017111

Processes

viral capsid assemblyGO:0019069

Locations

host cell cytoplasmGO:0030430

Translocates the three (+)ssRNA genome segments into the procapsid in sequential order.

Co-replicative ssDNA or RNA-operator-nucleated encapsidation (MS2/Qbeta/phiX174-type)Biological Processco_replicative_ssdna_ssrna_encapsidation

Tailless ssRNA leviviruses (MS2, Qbeta) and ssDNA microviruses (phiX174) lack an ATP-driven portal/terminase motor; instead, genomic ssRNA stem-loop operators nucleate coat-protein dimer assembly directly, or rolling-circle ssDNA displacement synthesis is coupled directly to procapsid encapsidation via gpJ/gpF.

Annotons

RNA-operator or ssDNA-coupled capsid encapsidation
coat_operator_or_ssdna_coupled_encapsidation
Participant: Any With Function: cp (Emesvirus zinderi)
Gene Product:
cp (Emesvirus zinderi)UniProtKB:P03612
Required Function:
structural constituent of virionGO:0039660
Coat protein subunits (such as MS2 cp or phiX174 F/J) bind viral genomic RNA operator hairpins or nascent displaced ssDNA to couple genome encapsidation with capsid assembly without an ATPase packaging motor.

Function

structural constituent of virionGO:0039660

Processes

viral capsid assemblyGO:0019069

Locations

host cell cytoplasmGO:0030430

Couples viral genome encapsidation directly to icosahedral shell assembly without a portal/terminase motor.