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- PDB-9mu3: SaPI1 neck structure -

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Basic information

Entry
Database: PDB / ID: 9mu3
TitleSaPI1 neck structure
Components
  • DUF3168 domain-containing protein
  • Head-tail connector protein
  • Major tail protein
  • adaptor
KeywordsVIRUS LIKE PARTICLE / sapi / capsid / tail / phage
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsKizziah, J.L. / Dokland, T.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Head-tail connector protein
B: Head-tail connector protein
C: adaptor
D: DUF3168 domain-containing protein
E: Major tail protein
F: Major tail protein


Theoretical massNumber of molelcules
Total (without water)95,2686
Polymers95,2686
Non-polymers00
Water00
1
A: Head-tail connector protein
B: Head-tail connector protein
C: adaptor
D: DUF3168 domain-containing protein
E: Major tail protein
F: Major tail protein
x 6


Theoretical massNumber of molelcules
Total (without water)571,61036
Polymers571,61036
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein Head-tail connector protein


Mass: 12809.583 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: UniProt: S4V9M2
#2: Protein adaptor


Mass: 11815.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: UniProt: A0AA96SLM5
#3: Protein DUF3168 domain-containing protein / tail completion protein


Mass: 14730.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: UniProt: A4ZFB8
#4: Protein Major tail protein


Mass: 21551.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: UniProt: A4ZFB9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Staphylococcus phage 80alpha / Type: VIRUS / Details: SaPI1 virion / Entity ID: all / Source: NATURAL
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 35.26 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23206 / Symmetry type: POINT

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