+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43278 | |||||||||
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Title | Cryo-EM of tail of bacteriophage Chi | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Flagellotropic bacteriophage / Siphophage / Tail / VIRUS | |||||||||
Function / homology | Bacterial 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 species | Chivirus chi | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Sonani RR / Esteves NC / Scharf BE / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43278.map.gz | 778.4 MB | EMDB map data format | |
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Header (meta data) | emd-43278-v30.xml emd-43278.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43278_fsc.xml | 19.8 KB | Display | FSC data file |
Images | emd_43278.png | 45.7 KB | ||
Filedesc metadata | emd-43278.cif.gz | 5.1 KB | ||
Others | emd_43278_half_map_1.map.gz emd_43278_half_map_2.map.gz | 764.9 MB 764.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43278 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43278 | HTTPS FTP |
-Validation report
Summary document | emd_43278_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_43278_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_43278_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | emd_43278_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43278 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43278 | HTTPS FTP |
-Related structure data
Related structure data | 8vjaMC 8vhxC 8vjhC 8vjiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43278.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_43278_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43278_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chivirus chi
Entire | Name: Chivirus chi |
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Components |
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-Supramolecule #1: Chivirus chi
Supramolecule | Name: 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
Macromolecule | Name: Tail Tube / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chivirus chi |
Molecular weight | Theoretical: 40.375363 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
Details | Tail of bacteriophage Chi |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |