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- EMDB-28130: Capsid structure of Staphylococcus phage Andhra -

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Basic information

Entry
Database: EMDB / ID: EMD-28130
TitleCapsid structure of Staphylococcus phage Andhra
Map data
Sample
  • Virus: Staphylococcus phage Andhra (virus)
    • Protein or peptide: gp19, capsid lining protein
    • Protein or peptide: Major capsid protein
Keywordsphage capsid / HK97-like fold / VIRUS
Function / homologyPhi29-like phage major capsid protein / Major capsid protein / Uncharacterized protein
Function and homology information
Biological speciesStaphylococcus phage Andhra (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHawkins NC / Kizziah JL / 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_28130.png

Downloads & links

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Map

FileDownload / File: emd_28130.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 679.936 Å		1.33 Å/pix.
x 512 pix.
= 679.936 Å		1.33 Å/pix.
x 512 pix.
= 679.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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-0.11632492 - 0.14884613
Average (Standard dev.)0.0006461096 (±0.007120261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 679.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28130_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28130_half_map_2.map
Projections & Slices
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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: gp19, capsid lining protein
    • Protein or peptide: Major capsid 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: gp19, capsid lining protein

MacromoleculeName: gp19, capsid lining protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 7.141647 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString:
MANFDGNEMR GMTHANYEDS RLNKSRELNA NMSIGTSKSE DEYGRQVHSL TKQSYSDDSV QEA

UniProtKB: Uncharacterized protein

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage Andhra (virus)
Molecular weightTheoretical: 46.35309 KDa
Recombinant expressionOrganism: Staphylococcus phage Andhra (virus)
SequenceString: MADKKTDIPT LIADSTKASL QDFNHDYGKQ WTFGENWSNV NTMFETYVNK YLFPKINETL LIDIALGNRF NWLAKEQDFI GQYSEEYVI MDTIPIEMNL SKSEELMLKR NYPQMATRLY GSGIVKKQKF TLNNNDVRFN FQTLGDATNY ALGVLRKKIS D INVQEEKE ...String:
MADKKTDIPT LIADSTKASL QDFNHDYGKQ WTFGENWSNV NTMFETYVNK YLFPKINETL LIDIALGNRF NWLAKEQDFI GQYSEEYVI MDTIPIEMNL SKSEELMLKR NYPQMATRLY GSGIVKKQKF TLNNNDVRFN FQTLGDATNY ALGVLRKKIS D INVQEEKE IRAMMVDYAI NQLQDSNRRT ASSKEDLTER VFEAILNMQN NSAKYNEVHK ASGGSVGQYT TVSKLSDIAI LT TDSLKSY LLDTKIANTF QMAGIDFTDH IISFDDLGGV YKTTKDVTLA NEDTINYLRA FGDYQAMIGD VIPTGSVFTF NVS DLKEFK GNIEEIKPQG ELFAFIFDIN ALKYKRNTKG MLKEPFYNGE FDEVTHWIHY YSFKAMSPFF NKILITEAPK EQPD AGATE

UniProtKB: Major capsid 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90677
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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