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- EMDB-43278: Cryo-EM of tail of bacteriophage Chi -

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Basic information

Entry
Database: EMDB / ID: EMD-43278
TitleCryo-EM of tail of bacteriophage Chi
Map data
Sample
  • Virus: Chivirus chi
    • Protein or peptide: Tail Tube
KeywordsFlagellotropic bacteriophage / Siphophage / Tail / VIRUS
Function / homologyBacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Invasin/intimin cell-adhesion fragments / Immunoglobulin-like fold / Major tail protein
Function and homology information
Biological speciesChivirus chi
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSonani RR / Esteves NC / Scharf BE / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Structure / Year: 2024
Title: Cryo-EM structure of flagellotropic bacteriophage Chi.
Authors: Ravi R Sonani / Nathaniel C Esteves / Birgit E Scharf / Edward H Egelman /
Abstract: The flagellotropic bacteriophage χ (Chi) infects bacteria via the flagellar filament. Despite years of study, its structural architecture remains partly characterized. Through cryo-EM, we unveil ...The flagellotropic bacteriophage χ (Chi) infects bacteria via the flagellar filament. Despite years of study, its structural architecture remains partly characterized. Through cryo-EM, we unveil χ's nearly complete structure, encompassing capsid, neck, tail, and tail tip. While the capsid and tail resemble phage YSD1, the neck and tail tip reveal new proteins and their arrangement. The neck shows a unique conformation of the tail tube protein, forming a socket-like structure for attachment to the neck. The tail tip comprises four proteins, including distal tail protein (DTP), two baseplate hub proteins (BH1P and BH2P), and tail tip assembly protein (TAP) exhibiting minimal organization compared to other siphophages. Deviating from the consensus in other siphophages, DTP in χ forms a trimeric assembly, reducing tail symmetry from 6-fold to 3-fold at the tip. These findings illuminate the previously unexplored structural organization of χ's neck and tail tip.
History
DepositionJan 6, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43278.png

Downloads & links

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Map

FileDownload / File: emd_43278.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.48679072 - 0.8981828
Average (Standard dev.)0.000625645 (±0.024773626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 492.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43278_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43278_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Chivirus chi

EntireName: Chivirus chi
Components
  • Virus: Chivirus chi
    • Protein or peptide: Tail Tube

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Supramolecule #1: Chivirus chi

SupramoleculeName: Chivirus chi / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1541887 / Sci species name: Chivirus chi / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tail Tube

MacromoleculeName: Tail Tube / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 40.375363 KDa
SequenceString: MNDNYQNNYV VGRGTVYFDR FQDGTNRKTG EMYFGNTPEF TINTDSETLD HYSSDHGMRV MDASVLLEAS QGGTFTCDNI NADNLALWF LGEVSNTTQT QQTDAKEVFN PIMRGRYYQL GTTDDNPTGV RGVTNFQMVK ADASIAISVG SGDITSIVGA T VVNPAGNY ...String:
MNDNYQNNYV VGRGTVYFDR FQDGTNRKTG EMYFGNTPEF TINTDSETLD HYSSDHGMRV MDASVLLEAS QGGTFTCDNI NADNLALWF LGEVSNTTQT QQTDAKEVFN PIMRGRYYQL GTTDDNPTGV RGVTNFQMVK ADASIAISVG SGDITSIVGA T VVNPAGNY EIDLEAGRIY IEPDSTDLSG NVQIAVQYDV DAQKRTLVIG KSNMVYGALR MISDNPVGLN KNYYFPKVSI AP DGDYALK GDDWQVMSFT FKAMQLNNIT QRVYIDIVEA AAAVDPTAQR TIEITPASTT ATTGGAGVVC TVTVRDGTGT AVQ GDAVTF TTVAGATVTP NSATTGATGT ATTTVNRAAA GTATVTATLA NGKAATTGTI TFSAP

UniProtKB: Major tail protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE
DetailsTail of bacteriophage Chi

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 40.86 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.83 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83657
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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