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- PDB-8t1x: T4 highly immunogenic outer capsid protein C-terminal domain boun... -

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Basic information

Entry
Database: PDB / ID: 8t1x
TitleT4 highly immunogenic outer capsid protein C-terminal domain bound to the vertex-proximal gp23* capsomer of the isometric head in two preferred orientations
Components
  • Highly immunogenic outer capsid protein
  • Mature major capsid protein gp23*
KeywordsVIRAL PROTEIN / bacteriophage / capsid / T4 head / Hoc / highly immunogenic outer capsid protein / virus decoration protein / immunoglobulin-like domains / antigen display / vaccine
Function / homology
Function and homology information


viral capsid, decoration / T=13 icosahedral viral capsid / viral capsid
Similarity search - Function
Highly immunogenic outer capsid protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Ig-like domain profile. ...Highly immunogenic outer capsid protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Highly immunogenic outer capsid protein / Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFokine, A. / Rao, V.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Viruses / Year: 2023
Title: Structure and Function of Hoc-A Novel Environment Sensing Device Encoded by T4 and Other Bacteriophages.
Authors: Andrei Fokine / Mohammad Zahidul Islam / Qianglin Fang / Zhenguo Chen / Lei Sun / Venigalla B Rao /
Abstract: Bacteriophage T4 is decorated with 155 180 Å-long fibers of the highly antigenic outer capsid protein (Hoc). In this study, we describe a near-atomic structural model of Hoc by combining cryo- ...Bacteriophage T4 is decorated with 155 180 Å-long fibers of the highly antigenic outer capsid protein (Hoc). In this study, we describe a near-atomic structural model of Hoc by combining cryo-electron microscopy and AlphaFold structure predictions. It consists of a conserved C-terminal capsid-binding domain attached to a string of three variable immunoglobulin (Ig)-like domains, an architecture well-preserved in hundreds of Hoc molecules found in phage genomes. Each T4-Hoc fiber attaches randomly to the center of gp23* hexameric capsomers in one of the six possible orientations, though at the vertex-proximal hexamers that deviate from 6-fold symmetry, Hoc binds in two preferred orientations related by 180° rotation. Remarkably, each Hoc fiber binds to all six subunits of the capsomer, though the interactions are greatest with three of the subunits, resulting in the off-centered attachment of the C-domain. Biochemical analyses suggest that the acidic Hoc fiber (pI, ~4-5) allows for the clustering of virions in acidic pH and dispersion in neutral/alkaline pH. Hoc appears to have evolved as a sensing device that allows the phage to navigate its movements through reversible clustering-dispersion transitions so that it reaches its destination, the host bacterium, and persists in various ecological niches such as the human/mammalian gut.
History
DepositionJun 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Highly immunogenic outer capsid protein
Y: Highly immunogenic outer capsid protein
A: Mature major capsid protein gp23*
B: Mature major capsid protein gp23*
C: Mature major capsid protein gp23*
D: Mature major capsid protein gp23*
E: Mature major capsid protein gp23*
F: Mature major capsid protein gp23*


Theoretical massNumber of molelcules
Total (without water)373,2068
Polymers373,2068
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Highly immunogenic outer capsid protein


Mass: 40416.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SW08
#2: Protein
Mature major capsid protein gp23* / gp23*


Mass: 48728.863 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P04535

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia phage T4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T4 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 18000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 26 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategoryDetails
7Cootmodel fitting
19PHENIXmodel refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19000 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322636
ELECTRON MICROSCOPYf_angle_d0.6230674
ELECTRON MICROSCOPYf_dihedral_angle_d4.8443168
ELECTRON MICROSCOPYf_chiral_restr0.0433346
ELECTRON MICROSCOPYf_plane_restr0.0044044

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