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- EMDB-43282: Cryo-EM of capsid of bacteriophage Chi -

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Basic information

Entry
Database: EMDB / ID: EMD-43282
TitleCryo-EM of capsid of bacteriophage Chi
Map data
Sample
  • Virus: Chivirus chi
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Decorator protein D
KeywordsFlagellotropic bacteriophage / Siphophage / Capsid / VIRUS
Function / homologyHead decoration protein D / Bacteriophage lambda head decoration protein D / Major capsid protein GpE / Phage major capsid protein E / viral capsid / host cell cytoplasm / Decorator protein D / Major capsid protein
Function and homology information
Biological speciesChivirus chi
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_43282.png

Downloads & links

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Map

FileDownload / File: emd_43282.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 768 pix.
= 819.994 Å		1.07 Å/pix.
x 768 pix.
= 819.994 Å		1.07 Å/pix.
x 768 pix.
= 819.994 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0677 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.51162916 - 1.029425
Average (Standard dev.)0.013243433 (±0.064313926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 819.99365 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43282_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43282_half_map_2.map
Projections & Slices
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Density Histograms

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: Major capsid protein
    • Protein or peptide: Decorator protein D

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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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 39.959625 KDa
SequenceString: MAGLYTTYQL LEVQRKLKTL PAFFLQWFPR QINFQEDMIA FDKVIQDVTR VAPFVAPNVQ GRVIKESGYN TKTFKPAYVK PKHVIDPNM IIPRQPGEAL GTGTLSIAQR RDRVIAYLLM KHRAMHENTW EWMAAQAAQY GYVDVQGQDY PLVRVDFGRD A ALTMTTDW ...String:
MAGLYTTYQL LEVQRKLKTL PAFFLQWFPR QINFQEDMIA FDKVIQDVTR VAPFVAPNVQ GRVIKESGYN TKTFKPAYVK PKHVIDPNM IIPRQPGEAL GTGTLSIAQR RDRVIAYLLM KHRAMHENTW EWMAAQAAQY GYVDVQGQDY PLVRVDFGRD A ALTMTTDW TAAGVTLMDM IADLRDGQRL VSDKSMSGTV IRDYIFGGDA WDQFVKVGGK ELWGKDGLMD STIRGSETNV TR LWDDVEG VQYMGELVGA NGAGRMRIWV NTQKYRDQND QEQFLMKQKA VMGISSAIEG VRCFGAILDK GAGYQALDYF PKM WDQEDP SVEYLMSQGA PLMVPADPNA SFLLTVMS

UniProtKB: Major capsid protein

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Macromolecule #2: Decorator protein D

MacromoleculeName: Decorator protein D / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 14.401047 KDa
SequenceString:
MNLLTMMAAT SLPNYLAGNG DLGSWEPTQI FAGEADIVTE GGAAGADIEI YQVIAKNAAG AMVPHDPTAT TGTSPDEVPA PQSVAIGIA AQPAKSGQNV PYYIGGVFNH AALGWHASLD TLAKRQAVFD RTNIHIGNLY

UniProtKB: Decorator protein D

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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: 8
VitrificationCryogen name: ETHANE
DetailsCapsid 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28512
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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