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- EMDB-28176: Tail tip structure of Staphylococcus phage Andhra -

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Basic information

Entry
Database: EMDB / ID: EMD-28176
TitleTail tip structure of Staphylococcus phage Andhra
Map data
Sample
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: gp1, tail tip protein
    • Protein or peptide: gp10, tail tip lysin (spike)
Keywordsphage tail / VIRUS
Function / homologyCHAP domain profile. / CHAP domain / CHAP domain / Peptidase
Function and homology information
Biological speciesStaphylococcus phage Andhra (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsKizziah JL / Hawkins NC / Dokland T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI156636 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure and host specificity of bacteriophage Andhra.
Authors: N'Toia C Hawkins / James L Kizziah / Asma Hatoum-Aslan / Terje Dokland /
Abstract: is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages ... is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion of -infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of 11 capsid and tail proteins. The capsid is a = 4 icosahedron containing a unique stabilizing capsid lining protein. The tail includes 12 trimers of a unique receptor binding protein (RBP), a lytic protein that also serves to anchor the RBPs to the tail stem, and a hexameric tail knob that acts as a gatekeeper for DNA ejection. Using structure prediction with AlphaFold, we identified the two proteins that comprise the tail tip heterooctamer. Our findings elucidate critical features for virion assembly, host recognition, and penetration.
History
DepositionSep 16, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28176.png

Downloads & links

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Map

FileDownload / File: emd_28176.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 256 pix.
= 339.968 Å		1.33 Å/pix.
x 256 pix.
= 339.968 Å		1.33 Å/pix.
x 256 pix.
= 339.968 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.048139088 - 0.07593109
Average (Standard dev.)0.000016834068 (±0.0032397346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 339.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28176_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28176_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : Staphylococcus phage Andhra

EntireName: Staphylococcus phage Andhra (virus)
Components
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: gp1, tail tip protein
    • Protein or peptide: gp10, tail tip lysin (spike)

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Supramolecule #1: Staphylococcus phage Andhra

SupramoleculeName: Staphylococcus phage Andhra / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2, #1 / NCBI-ID: 1958907 / Sci species name: Staphylococcus phage Andhra / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus epidermidis (bacteria)

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Macromolecule #1: gp10, tail tip lysin (spike)

MacromoleculeName: gp10, tail tip lysin (spike) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 51.675402 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: MNDKEKIDKF IHSNLNDDFG LSVDDLVGKV KGIGRFSAWC GNSSTKIKQV LNAVKSIGVS PALFAAYEKN EGYNGSWGWL NHTSPQGNY LTDAQFVARK LVSQSRQAGT PSWIDAGNPV DFVPASVKRK GNYDFSHNMK NGKVGRAYIP LTAAATWAAY Y PEGLQASY ...String:
MNDKEKIDKF IHSNLNDDFG LSVDDLVGKV KGIGRFSAWC GNSSTKIKQV LNAVKSIGVS PALFAAYEKN EGYNGSWGWL NHTSPQGNY LTDAQFVARK LVSQSRQAGT PSWIDAGNPV DFVPASVKRK GNYDFSHNMK NGKVGRAYIP LTAAATWAAY Y PEGLQASY NRVQNYGNPF LDAANTILGW GGKIDGKGGS SSGSSSSSSG TSGGLDVVAR AFEEFLKKLQ DSMQWDLHSI GT DKFFSNQ MFTITKTYNN TYRLNMNQKL LDEMKDLISR IDGGSGNDTG ADDSDGDHGG KAGKSVAPNG KSGRKIGGNW TYS NLPQKY KDAIEVPKFD PKYLAGSPFV NTGDTGQCTE LTWAYMHQIW GKRQPAWDNQ VTNGQRVWVV YRNQGARVTH RPTV GYGFS SKPNYLQAML PGVGHTGVVV AVFKDGSFLT ANYNVPPYWA PSRVVEYALI DGVPENAGDN IMFFSGIK

UniProtKB: Peptidase

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Macromolecule #2: gp1, tail tip protein

MacromoleculeName: gp1, tail tip protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 10.640743 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString:
VTNEKGQAYT EMLQLFNLLQ QWNDFYTAEN ANNLLVACQQ LLINYNEPVI KFINDENEDK SLLQYLAGDD GLAQWQFYKG FYNNYNVHI F

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 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: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98203
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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