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- PDB-8gmo: Bacteriophage T4 capsid shell containing 9DE insertions into the ... -

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Basic information

Entry
Database: PDB / ID: 8gmo
TitleBacteriophage T4 capsid shell containing 9DE insertions into the gp23* major capsid protein subunits
Components
  • Mature capsid vertex protein
  • Mature major capsid protein
KeywordsVIRUS LIKE PARTICLE / Bacteriophage T4 / capsid shell / phage display / decorated capsid / phage head
Function / homologyCapsid vertex protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / T=13 icosahedral viral capsid / viral capsid / Major capsid protein / Capsid vertex protein
Function and homology information
Biological speciesTequatrovirus T4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFokine, A. / Rao, V.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI111538 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
National Science Foundation (NSF, United States)MCB-0923873 United States
CitationJournal: Nat Commun / Year: 2023
Title: Design of bacteriophage T4-based artificial viral vectors for human genome remodeling.
Authors: Jingen Zhu / Himanshu Batra / Neeti Ananthaswamy / Marthandan Mahalingam / Pan Tao / Xiaorong Wu / Wenzheng Guo / Andrei Fokine / Venigalla B Rao /
Abstract: Designing artificial viral vectors (AVVs) programmed with biomolecules that can enter human cells and carry out molecular repairs will have broad applications. Here, we describe an assembly-line ...Designing artificial viral vectors (AVVs) programmed with biomolecules that can enter human cells and carry out molecular repairs will have broad applications. Here, we describe an assembly-line approach to build AVVs by engineering the well-characterized structural components of bacteriophage T4. Starting with a 120 × 86 nm capsid shell that can accommodate 171-Kbp DNA and thousands of protein copies, various combinations of biomolecules, including DNAs, proteins, RNAs, and ribonucleoproteins, are externally and internally incorporated. The nanoparticles are then coated with cationic lipid to enable efficient entry into human cells. As proof of concept, we assemble a series of AVVs designed to deliver full-length dystrophin gene or perform various molecular operations to remodel human genome, including genome editing, gene recombination, gene replacement, gene expression, and gene silencing. These large capacity, customizable, multiplex, and all-in-one phage-based AVVs represent an additional category of nanomaterial that could potentially transform gene therapies and personalized medicine.
History
DepositionMar 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.initial_refinement_model_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Mature major capsid protein
1: Mature major capsid protein
2: Mature major capsid protein
3: Mature major capsid protein
4: Mature major capsid protein
5: Mature major capsid protein
6: Mature major capsid protein
7: Mature major capsid protein
8: Mature major capsid protein
9: Mature major capsid protein
A: Mature capsid vertex protein
AA: Mature major capsid protein
AB: Mature major capsid protein
AC: Mature major capsid protein
AD: Mature major capsid protein
AE: Mature major capsid protein
AF: Mature major capsid protein
AG: Mature major capsid protein
AH: Mature major capsid protein
AI: Mature major capsid protein
AJ: Mature major capsid protein
AK: Mature major capsid protein
AL: Mature major capsid protein
AM: Mature major capsid protein
AN: Mature major capsid protein
AO: Mature major capsid protein
AP: Mature major capsid protein
AQ: Mature major capsid protein
AR: Mature major capsid protein
AS: Mature major capsid protein
AT: Mature major capsid protein
AU: Mature major capsid protein
AV: Mature major capsid protein
AW: Mature major capsid protein
AX: Mature major capsid protein
AY: Mature major capsid protein
AZ: Mature major capsid protein
Aa: Mature major capsid protein
Ab: Mature major capsid protein
Ac: Mature major capsid protein
Ad: Mature major capsid protein
Ae: Mature major capsid protein
Af: Mature major capsid protein
Ag: Mature major capsid protein
Ah: Mature major capsid protein
Ai: Mature major capsid protein
Aj: Mature major capsid protein
Ak: Mature major capsid protein
Al: Mature major capsid protein
Am: Mature major capsid protein
B: Mature capsid vertex protein
C: Mature capsid vertex protein
D: Mature capsid vertex protein
G: Mature major capsid protein
H: Mature major capsid protein
J: Mature major capsid protein
K: Mature major capsid protein
L: Mature major capsid protein
M: Mature major capsid protein
N: Mature major capsid protein
O: Mature major capsid protein
P: Mature major capsid protein
Q: Mature major capsid protein
R: Mature major capsid protein
S: Mature major capsid protein
T: Mature major capsid protein
U: Mature major capsid protein
V: Mature major capsid protein
W: Mature major capsid protein
X: Mature major capsid protein
Y: Mature major capsid protein
Z: Mature major capsid protein
a: Mature capsid vertex protein
b: Mature major capsid protein
c: Mature major capsid protein
d: Mature major capsid protein
e: Mature major capsid protein
f: Mature major capsid protein
g: Mature major capsid protein
h: Mature major capsid protein
i: Mature major capsid protein
j: Mature major capsid protein
k: Mature major capsid protein
l: Mature major capsid protein
m: Mature major capsid protein
n: Mature major capsid protein
o: Mature major capsid protein
p: Mature major capsid protein
q: Mature major capsid protein
r: Mature major capsid protein
s: Mature major capsid protein
t: Mature major capsid protein
u: Mature major capsid protein
v: Mature major capsid protein
w: Mature major capsid protein
x: Mature major capsid protein
y: Mature major capsid protein
z: Mature major capsid protein


Theoretical massNumber of molelcules
Total (without water)4,858,50998
Polymers4,858,50998
Non-polymers00
Water00
1
0: Mature major capsid protein
1: Mature major capsid protein
2: Mature major capsid protein
3: Mature major capsid protein
4: Mature major capsid protein
5: Mature major capsid protein
6: Mature major capsid protein
7: Mature major capsid protein
8: Mature major capsid protein
9: Mature major capsid protein
A: Mature capsid vertex protein
AA: Mature major capsid protein
AB: Mature major capsid protein
AC: Mature major capsid protein
AD: Mature major capsid protein
AE: Mature major capsid protein
AF: Mature major capsid protein
AG: Mature major capsid protein
AH: Mature major capsid protein
AI: Mature major capsid protein
AJ: Mature major capsid protein
AK: Mature major capsid protein
AL: Mature major capsid protein
AM: Mature major capsid protein
AN: Mature major capsid protein
AO: Mature major capsid protein
AP: Mature major capsid protein
AQ: Mature major capsid protein
AR: Mature major capsid protein
AS: Mature major capsid protein
AT: Mature major capsid protein
AU: Mature major capsid protein
AV: Mature major capsid protein
AW: Mature major capsid protein
AX: Mature major capsid protein
AY: Mature major capsid protein
AZ: Mature major capsid protein
Aa: Mature major capsid protein
Ab: Mature major capsid protein
Ac: Mature major capsid protein
Ad: Mature major capsid protein
Ae: Mature major capsid protein
Af: Mature major capsid protein
Ag: Mature major capsid protein
Ah: Mature major capsid protein
Ai: Mature major capsid protein
Aj: Mature major capsid protein
Ak: Mature major capsid protein
Al: Mature major capsid protein
Am: Mature major capsid protein
B: Mature capsid vertex protein
C: Mature capsid vertex protein
D: Mature capsid vertex protein
G: Mature major capsid protein
H: Mature major capsid protein
J: Mature major capsid protein
K: Mature major capsid protein
L: Mature major capsid protein
M: Mature major capsid protein
N: Mature major capsid protein
O: Mature major capsid protein
P: Mature major capsid protein
Q: Mature major capsid protein
R: Mature major capsid protein
S: Mature major capsid protein
T: Mature major capsid protein
U: Mature major capsid protein
V: Mature major capsid protein
W: Mature major capsid protein
X: Mature major capsid protein
Y: Mature major capsid protein
Z: Mature major capsid protein
a: Mature capsid vertex protein
b: Mature major capsid protein
c: Mature major capsid protein
d: Mature major capsid protein
e: Mature major capsid protein
f: Mature major capsid protein
g: Mature major capsid protein
h: Mature major capsid protein
i: Mature major capsid protein
j: Mature major capsid protein
k: Mature major capsid protein
l: Mature major capsid protein
m: Mature major capsid protein
n: Mature major capsid protein
o: Mature major capsid protein
p: Mature major capsid protein
q: Mature major capsid protein
r: Mature major capsid protein
s: Mature major capsid protein
t: Mature major capsid protein
u: Mature major capsid protein
v: Mature major capsid protein
w: Mature major capsid protein
x: Mature major capsid protein
y: Mature major capsid protein
z: Mature major capsid protein
x 10


  • complete point assembly
  • 48.6 MDa, 980 polymers
Theoretical massNumber of molelcules
Total (without water)48,585,095980
Polymers48,585,095980
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation9
2


  • Idetical with deposited unit
  • point asymmetric unit
  • Evidence: electron microscopy, The T4 capsid shell can be generated by applying the D5 symmetry.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D5 (2x5 fold dihedral))

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Components

#1: Protein ...
Mature major capsid protein / gp23*


Mass: 49790.727 Da / Num. of mol.: 93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus T4 / Gene: gp23 / Production host: Escherichia coli (E. coli) / References: UniProt: P04535
#2: Protein
Mature capsid vertex protein / gp24*


Mass: 45594.375 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus T4 / Gene: 24 / Production host: Escherichia coli (E. coli) / References: UniProt: P19896

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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: Enterobacteria phage T4 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Enterobacteria phage T4 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3.1particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinementphenix_real_space_refine
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70340
Details: The reconstruction was performed using RELION 3.1. The map was sharpened with an automatically calculated B-factor of -129 A2 using the RELION post-processing tool.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 7VS5

7vs5


Accession code: 7VS5 / Source name: PDB / Type: experimental model

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