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- EMDB-48618: SaPI1 neck structure -

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Basic information

Entry
Database: EMDB / ID: EMD-48618
TitleSaPI1 neck structure
Map data
Sample
  • Virus: Staphylococcus phage 80alpha (virus)
    • Protein or peptide: Head-tail connector protein
    • Protein or peptide: adaptor
    • Protein or peptide: DUF3168 domain-containing protein
    • Protein or peptide: Major tail protein
Keywordssapi / capsid / tail / phage / VIRUS LIKE PARTICLE
Function / homologyBacteriophage 69, Orf23, major tail protein / Phage gp6-like head-tail connector protein / Phage gp6-like head-tail connector protein / Phage major tail protein TP901-1 / Phage tail tube protein / Uncharacterized protein / DUF3168 domain-containing protein / Major tail protein / Head-tail connector protein
Function and homology information
Biological speciesStaphylococcus phage 80alpha (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsKizziah JL / Dokland T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI083255 United States
CitationJournal: Structure / Year: 2025
Title: Structure of the Staphylococcus aureus bacteriophage 80α neck shows details of the DNA, tail completion protein, and tape measure protein.
Authors: James L Kizziah / Amarshi Mukherjee / Laura K Parker / Terje Dokland /
Abstract: The Staphylococcus aureus pathogenicity islands (SaPIs), including SaPI1, are a type of mobile genetic elements (MGEs) that are mobilized at high frequency by "helper" bacteriophages, such as 80α, ...The Staphylococcus aureus pathogenicity islands (SaPIs), including SaPI1, are a type of mobile genetic elements (MGEs) that are mobilized at high frequency by "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from helper-encoded structural proteins. 80α and SaPI1 virions consist of an icosahedral head connected via a portal vertex to a long, non-contractile tail. A connector or "neck" forms the interface between the tail and the head. Here, we have determined the high-resolution structure of the neck section of SaPI1 virions, including the dodecameric portal and head-tail-connector proteins, and the hexameric head-tail joining, tail terminator and major tail proteins. We also resolved the DNA, the tail completion protein (TCP), and the tape measure protein (TMP) inside the tail, features that have not previously been observed at high resolution. Our study provides insights into the assembly and infection process in this important group of MGEs.
History
DepositionJan 13, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48618.png

Downloads & links

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Map

FileDownload / File: emd_48618.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 240 pix.
= 319.2 Å		1.33 Å/pix.
x 240 pix.
= 319.2 Å		1.33 Å/pix.
x 240 pix.
= 319.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-3.4314983 - 6.3417373
Average (Standard dev.)-0.018043544 (±0.25718445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 319.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48618_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_48618_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_48618_half_map_2.map
Projections & Slices
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Sample components

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Entire : Staphylococcus phage 80alpha

EntireName: Staphylococcus phage 80alpha (virus)
Components
  • Virus: Staphylococcus phage 80alpha (virus)
    • Protein or peptide: Head-tail connector protein
    • Protein or peptide: adaptor
    • Protein or peptide: DUF3168 domain-containing protein
    • Protein or peptide: Major tail protein

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Supramolecule #1: Staphylococcus phage 80alpha

SupramoleculeName: Staphylococcus phage 80alpha / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: SaPI1 virion / NCBI-ID: 2911440 / Sci species name: Staphylococcus phage 80alpha / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Head-tail connector protein

MacromoleculeName: Head-tail connector protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 12.809583 KDa
SequenceString:
MTTLADVKKR IGLKDEKQDE QLEEIIKSCE SQLLSMLPIE VEQIPERFSY MIKEVAVKRY NRIGAEGMTS EAVDGRSNAY ELNDFKEYE AIIDNYFNAR TRTKKGRAVF F

UniProtKB: Head-tail connector protein

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Macromolecule #2: adaptor

MacromoleculeName: adaptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 11.815448 KDa
SequenceString:
MRYEDRVIFQ LEQVATYNPK TSKKENTLIT YDAIPCNINP ISRARKQLEF GDVKNDVSVL RIKESISYPV SHVLVNGIRY KIVDTRIYR HETSYYIEEV N

UniProtKB: Uncharacterized protein

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Macromolecule #3: DUF3168 domain-containing protein

MacromoleculeName: DUF3168 domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 14.730251 KDa
SequenceString:
MTPNLQLYNK AYETLQGYGF PVISRKEMQQ EIPYPFFVIK MPESNRSKYT FDSYSGDTNL VIDIWSVSDD LGHHDGLVKR CIDDLTPSV KTNDYDFEED DTNITQLVDD TTNQELLHTS ITISYKTF

UniProtKB: DUF3168 domain-containing protein

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Macromolecule #4: Major tail protein

MacromoleculeName: Major tail protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 21.551746 KDa
SequenceString: MANMKNSNDR IILFRKAGEK VDATKMLFLT EYGLSHEADT DTEDTMDGSY NTGGSVESTM SGTAKMFYGD DFADEIEDAV VDRVLYEAW EVESRIPGKN GDSAKFKAKY FQGFHNKFEL KAEANGIDEY EYEYGVNGRF QRGFATLPEA VTKKLKATGY R FHDTTKED ...String:
MANMKNSNDR IILFRKAGEK VDATKMLFLT EYGLSHEADT DTEDTMDGSY NTGGSVESTM SGTAKMFYGD DFADEIEDAV VDRVLYEAW EVESRIPGKN GDSAKFKAKY FQGFHNKFEL KAEANGIDEY EYEYGVNGRF QRGFATLPEA VTKKLKATGY R FHDTTKED ALTSEDLTAI PQPKVDSSTV TPGEV

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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.26 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23206
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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