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- EMDB-28129: Tail knob structure of Staphylococcus phage Andhra -

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Basic information

Entry
Database: EMDB / ID: EMD-28129
TitleTail knob structure of Staphylococcus phage Andhra
Map data
Sample
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: Lower collar protein
    • Protein or peptide: Major tail protein
Keywordsphage tail / VIRUS
Function / homologyDistal tube protein, N-terminal / Caudoviral major tail protein N-terminus / Lower collar protein / Major tail protein
Function and homology information
Biological speciesStaphylococcus phage Andhra (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 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 13, 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_28129.png

Downloads & links

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Map

FileDownload / File: emd_28129.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.328 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.064230114 - 0.11635542
Average (Standard dev.)0.00015455898 (±0.00313146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 509.95197 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28129_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_28129_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Lower collar protein
    • Protein or peptide: Major tail protein

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Supramolecule #1: Staphylococcus phage Andhra

SupramoleculeName: Staphylococcus phage Andhra / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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: Lower collar protein

MacromoleculeName: Lower collar protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 28.450355 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: MQKMLYFDDD VKQIVDHMFF KGFMFNDERI DRYFKESFTL RFLYREIGRQ TVESFASQVL YITMTHEDYI YRVYGSDMYK YIEQVTDTQ SQDLGKAIEN AIEQGQTKDR QQDKGHEEYK DYEDTITKSF DDNRTAESTL PQSKVNIDVD NTVLDYADTN T ISRDKNTS ...String:
MQKMLYFDDD VKQIVDHMFF KGFMFNDERI DRYFKESFTL RFLYREIGRQ TVESFASQVL YITMTHEDYI YRVYGSDMYK YIEQVTDTQ SQDLGKAIEN AIEQGQTKDR QQDKGHEEYK DYEDTITKSF DDNRTAESTL PQSKVNIDVD NTVLDYADTN T ISRDKNTS ETVSEKTGTK DNTFDSLRNG ESDTKRNTQS QNEMNRTGLT KQYLIDNLQK LYSMRDTIFK TYDKECFLHI W

UniProtKB: Lower collar protein

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Macromolecule #2: Major tail protein

MacromoleculeName: Major tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 68.431773 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: MADRKLTHFK FFYNTPLTDY QNTIHFSSNN ERDNYFLNEN HFNAIDYKNI PFNFIRDRNM VNLEQMSWQD AQGINYCTFK SDFENRRYY AFVNQIEYVN DHVTRMYLVI DTVMTYTQGN VLSTVQNAFV ERQHLPRDVY NYLLPSLRNN DDVIKASNKY Y LNNYLEQF ...String:
MADRKLTHFK FFYNTPLTDY QNTIHFSSNN ERDNYFLNEN HFNAIDYKNI PFNFIRDRNM VNLEQMSWQD AQGINYCTFK SDFENRRYY AFVNQIEYVN DHVTRMYLVI DTVMTYTQGN VLSTVQNAFV ERQHLPRDVY NYLLPSLRNN DDVIKASNKY Y LNNYLEQF GGNLVLFQSS ADLSKKFGTK KEPNLESSKG ITYDYITSPV NLYVMNREDF NNFMDKMSKY PWITQNFQKI IL IPATFIN KDDLEAVKTQ EDIKGLMTLK NDKLSNEWEL KELRVPFERL QYMLNSNQDE LKHLVRNEYL TIEIYSWNGD SLL LDAGKI TERTGVKLKT KSIIGYHNEV RIYPVDYNSA PNEKPIKASD NSILIDTGSF LNTAITFDSF AEVPILIDNG LLAQ SQQAN KQKNAQSNLI SNRINNVVNG NDLKSRFYDA VSIGSNLSPT ALFSKFNDEY NYYKELRAEY KDLALQPPTV TSSQM GNAF QIANSINGLT MKIGVPAPFD MDNIQRYYFM LGFETNDQAG TPFPIDSWTV CNYLRMRGTY TIDGIDPMLL EQLKVL LET GVRFWHNDGT NNPMAQNVFK NKFRK

UniProtKB: Major tail protein

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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: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101037
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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