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- EMDB-40228: Bacteriophage T4 capsid shell containing 9DE insertions into the ... -

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Basic information

Entry
Database: EMDB / ID: EMD-40228
TitleBacteriophage T4 capsid shell containing 9DE insertions into the gp23* major capsid protein subunits
Map data
Sample
  • Virus: Enterobacteria phage T4 (virus)
    • Protein or peptide: Mature major capsid protein
    • Protein or peptide: Mature capsid vertex protein
KeywordsBacteriophage T4 / capsid shell / phage display / decorated capsid / phage head / VIRUS LIKE PARTICLE
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 / Enterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFokine A / Rao VB
Funding support United States, 3 items
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, 2023-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40228.png

Downloads & links

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Map

FileDownload / File: emd_40228.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.85 Å/pix.
x 720 pix.
= 1332. Å		1.85 Å/pix.
x 720 pix.
= 1332. Å		1.85 Å/pix.
x 720 pix.
= 1332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.048439845 - 0.08359766
Average (Standard dev.)0.00006757792 (±0.0045733885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 1332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40228_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40228_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40228_half_map_2.map
Projections & Slices
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Sample components

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Entire : Enterobacteria phage T4

EntireName: Enterobacteria phage T4 (virus)
Components
  • Virus: Enterobacteria phage T4 (virus)
    • Protein or peptide: Mature major capsid protein
    • Protein or peptide: Mature capsid vertex protein

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Mature major capsid protein

MacromoleculeName: Mature major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 93 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 49.790727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AEIGGDHGYN ATNIAAGQTS GAVTQIGPAV MGMVRRAIPN LIAFDICGVQ PMNSPTGQVF ALRAVYGKDP VAAGAKEAFH PMYGPDAMF SGQGAAKKFP ALAASTQTTV GDIYTHFFQE TGTVYLQASV QVTIDAGDED EDEDEDATDA AKLDAEIKKQ M EAGALVEI ...String:
AEIGGDHGYN ATNIAAGQTS GAVTQIGPAV MGMVRRAIPN LIAFDICGVQ PMNSPTGQVF ALRAVYGKDP VAAGAKEAFH PMYGPDAMF SGQGAAKKFP ALAASTQTTV GDIYTHFFQE TGTVYLQASV QVTIDAGDED EDEDEDATDA AKLDAEIKKQ M EAGALVEI AEGMATSIAE LQEGFNGSTD NPWNEMGFRI DKQVIEAKSR QLKAAYSIEL AQDLRAVHGM DADAELSGIL AT EIMLEIN REVVDWINYS AQVGKSGMTL TPGSKAGVFD FQDPIDIRGA RWAGESFKAL LFQIDKEAVE IARQTGRGEG NFI IASRNV VNVLASVDTG ISYAAQGLAT GFSTDTTKSV FAGVLGGKYR VYIDQYAKQD YFTVGYKGPN EMDAGIYYAP YVAL TPLRG SDPKNFQPVM GFKTRYGIGI NPFAESAAQA PASRIQSGMP SILNSLGKNA YFRRVYVKGI

UniProtKB: Major capsid protein

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Macromolecule #2: Mature capsid vertex protein

MacromoleculeName: Mature capsid vertex protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 45.594375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: STTTNSNSIG RPNLVALTRA TTKLIYSDIV ATQRTNQPVA AFYGIKYLNP DNEFTFKTGA TYAGEAGYVD REQITELTEE SKLTLNKGD LFKYNNIVYK VLEDTPFATI EESDLELALQ IAIVLLKVRL FSDAASTSKF ESSDSEIADA RFQINKWQTA V KSRKLKTG ...String:
STTTNSNSIG RPNLVALTRA TTKLIYSDIV ATQRTNQPVA AFYGIKYLNP DNEFTFKTGA TYAGEAGYVD REQITELTEE SKLTLNKGD LFKYNNIVYK VLEDTPFATI EESDLELALQ IAIVLLKVRL FSDAASTSKF ESSDSEIADA RFQINKWQTA V KSRKLKTG ITVELAQDLE ANGFDAPNFL EDLLATEMAD EINKDILQSL ITVSKRYKVT GITDSGFIDL SYASAPEAGR SL YRMVCEM VSHIQKESTY TATFCVASAR AAAILAASGW LKHKPEDDKY LSQNAYGFLA NGLPLYCDTN SPLDYVIVGV VEN IGEKEI VGSIFYAPYT EGLDLDDPEH VGAFKVVVDP ESLQPSIGLL VRYALSANPY TVAKDEKEAR IIDGGDMDKM AGRS DLSVL LGVKLPKIII

UniProtKB: Capsid vertex protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 64000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6323

Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
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.
Number images used: 70340
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7vs5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8gmo:
Bacteriophage T4 capsid shell containing 9DE insertions into the gp23* major capsid protein subunits

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