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- EMDB-47777: Cryo-EM reconstruction of Escherichia phage N4 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-47777
TitleCryo-EM reconstruction of Escherichia phage N4 capsid
Map data
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: 32 kDa protein
KeywordsBacteriophage / capsid / Hoc-like decoration protein / Ig-like decoration protein / Schitoviridae / N4 / enquatroviridae / VIRAL PROTEIN
Function / homologyviral capsid / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 32 kDa protein / Major capsid protein
Function and homology information
Biological speciesEscherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsEruera A / McJarrow-Keller K / Hyun JK / Bostina M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Viruses / Year: 2024
Title: Atlas of Interactions Between Decoration Proteins and Major Capsid Proteins of Coliphage N4.
Authors: Klem McJarrow-Keller / Alice-Roza Eruera / Alexander J M Crowe / Rosheny Kumaran / Jaekyung Hyun / Mihnea Bostina /
Abstract: Coliphage N4 is a representative species of the family of bacteriophages. Originally structurally studied in 2008, the capsid structure was solved to 14 Å to reveal an interesting arrangement of Ig- ...Coliphage N4 is a representative species of the family of bacteriophages. Originally structurally studied in 2008, the capsid structure was solved to 14 Å to reveal an interesting arrangement of Ig-like decoration proteins across the surface of the capsid. Herein, we present a high-resolution N4 structure, reporting a 2.45 Å map of the capsid obtained via single particle cryogenic-electron microscopy. Structural analysis of the major capsid proteins (MCPs) and decoration proteins (gp56 and gp17) of phage N4 reveals a pattern of interactions across the capsid that are mediated by structurally homologous domains of gp17. In this study, an analysis of the complex interface contacts allows us to confirm that the gp17 Ig-like decoration proteins of N4 are likely employed by the virus to increase the capsid's structural integrity.
History
DepositionNov 7, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47777.png

Downloads & links

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Map

FileDownload / File: emd_47777.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 1000 pix.
= 1067.3 Å		1.07 Å/pix.
x 1000 pix.
= 1067.3 Å		1.07 Å/pix.
x 1000 pix.
= 1067.3 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0673 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.385
Minimum - Maximum-1.6103933 - 2.86422
Average (Standard dev.)0.0040648705 (±0.12746035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1067.2999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47777_msk_1.map
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Half map: #2

Fileemd_47777_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_47777_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia phage N4

EntireName: Escherichia phage N4 (virus)
Components
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: 32 kDa protein

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Supramolecule #1: Escherichia phage N4

SupramoleculeName: Escherichia phage N4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Escherichia phage N4 expressed in E. coli K-12 / NCBI-ID: 2886925 / Sci species name: Escherichia phage N4 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 44.074816 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MLNYNAPTDG QKSSIDGANS DQMQTFFWLK KAIITARKEQ YFMPLASVTN MPKHYGKTIK VYEYVPLLDD RNINDQGIDA SGATIVNGN LYGSSKDIGN ITSKLPLLTE NGGRVNRVGF TRIAREGSIH KFGFFYEFTQ ESIDFDSDDG LMEHLSRELM N GATQITEA ...String:
MLNYNAPTDG QKSSIDGANS DQMQTFFWLK KAIITARKEQ YFMPLASVTN MPKHYGKTIK VYEYVPLLDD RNINDQGIDA SGATIVNGN LYGSSKDIGN ITSKLPLLTE NGGRVNRVGF TRIAREGSIH KFGFFYEFTQ ESIDFDSDDG LMEHLSRELM N GATQITEA VLQKDLLAAA GTVLYAGAAT SDATITGEGS TPSVVSYKNL MRLDQILTEN RTPTQTTIIT GSRMIDTKVI GA TRVMYVG SELVPELKAM KDLFGNKAFI ETQHYADAGT IMNGEVGSID KFRIIQVPEM LHWAGAGAQA TGANPGYRTS MVS GQEHYD VYPMLVVGDD SFTSIGFQTD GKSLKFTVMT KMPGKETADR NDPYGETGFS SIKWYYGILV KRPERLALIK TVAP L

UniProtKB: Major capsid protein

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Macromolecule #2: 32 kDa protein

MacromoleculeName: 32 kDa protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 29.2059 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MPVLKVMFHK DTNVATVLDA SGSLSDGSVE VGTFHHPDET YPDSVTIYHG VRDLLYKRSA KDPSQTASYP NNIINMQVIS IDMKATPRL ILGTALPRVI STIEGKDVTW HVDVAGGKAP LTYKWQFKAN TVGAAFADID SGENPTAKTA TLINHAVTAE S AGTYKVIV ...String:
MPVLKVMFHK DTNVATVLDA SGSLSDGSVE VGTFHHPDET YPDSVTIYHG VRDLLYKRSA KDPSQTASYP NNIINMQVIS IDMKATPRL ILGTALPRVI STIEGKDVTW HVDVAGGKAP LTYKWQFKAN TVGAAFADID SGENPTAKTA TLINHAVTAE S AGTYKVIV TDANGTTIES SSLLVVGVQE PPEVASIVAY PSPLALSVAD DITDGKTVKF SSLPAGSLIG TLSIKTQPDS GK ATAEISG NVLTVKPVAA GDTTVVVTNG TKEVTVTVNV TE

UniProtKB: 32 kDa 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: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 53.59 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: 2.0 µm / Nominal defocus min: 0.4 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 160000
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157663
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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