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- PDB-9e99: Cryo-EM reconstruction of Escherichia phage N4 capsid -

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Basic information

Entry
Database: PDB / ID: 9.0E+99
TitleCryo-EM reconstruction of Escherichia phage N4 capsid
Components
  • 32 kDa protein
  • Major capsid protein
KeywordsVIRAL PROTEIN / Bacteriophage / capsid / Hoc-like decoration protein / Ig-like decoration protein / Schitoviridae / N4 / enquatroviridae
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsEruera, A. / McJarrow-Keller, K. / Hyun, J.K. / Bostina, M.
Funding support1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: 32 kDa protein
K: 32 kDa protein
L: 32 kDa protein


Theoretical massNumber of molelcules
Total (without water)484,29112
Polymers484,29112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Major capsid protein / Gene product 56 / gp56 / Major head protein


Mass: 44074.816 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage N4 (virus) / Gene: 56 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q859Q5
#2: Protein 32 kDa protein


Mass: 29205.900 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage N4 (virus) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0MZA7
Has protein modificationN

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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 N4 / Type: VIRUS / Details: Escherichia phage N4 expressed in E. coli K-12 / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage N4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 53.59 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 160000
3D reconstructionResolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157663 / Symmetry type: POINT

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