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- PDB-9mu2: SaPI1 neck structure with DNA, tail completion protein, and tape ... -

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Basic information

Entry
Database: PDB / ID: 9mu2
TitleSaPI1 neck structure with DNA, tail completion protein, and tape measure protein
Components
  • DNA, 3'-5'
  • DNA, 5'-3'
  • DUF3168 domain-containing protein
  • HK97 gp10 family phage protein
  • Head-tail connector protein
  • Major tail protein
  • Tape measure protein
  • adaptor
KeywordsVIRUS LIKE PARTICLE / sapi / capsid / tail / phage
Function / homology
Function and homology information


Bacteriophage HK97-gp10, putative tail-component / Bacteriophage HK97-gp10, putative tail-component / Bacteriophage 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 / Armadillo-type fold
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / DNA (> 1000) / HK97 gp10 family phage protein / Uncharacterized protein / DUF3168 domain-containing protein / Major tail protein / Tape measure protein / Head-tail connector protein
Similarity search - Component
Biological speciesStaphylococcus phage 80alpha (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 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
Citation
Journal: 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.
#1: Journal: bioRxiv / Year: 2024
Title: Structure of the bacteriophage 80α neck shows the interactions between DNA, tail completion protein and tape measure protein.
Authors: James L Kizziah / Amarshi Mukherjee / Laura K Parker / Terje Dokland /
Abstract: Tailed bacteriophages with double-stranded DNA genomes (class ) play an important role in the evolution of bacterial pathogenicity, both as carriers of genes encoding virulence factors and as the ...Tailed bacteriophages with double-stranded DNA genomes (class ) play an important role in the evolution of bacterial pathogenicity, both as carriers of genes encoding virulence factors and as the main means of horizontal transfer of mobile genetic elements (MGEs) in many bacteria, such as . The pathogenicity islands (SaPIs), including SaPI1, are a type of MGEs are that carry a variable complement of genes encoding virulence factors. SaPI1 is mobilized at high frequency by "helper" bacteriophages, such as 80α, leading to packaging of the SaPI1 genome into virions made from structural proteins supplied by the helper. 80α and SaPI1 virions consist of an icosahedral head (capsid) connected via a unique vertex to a long, non-contractile tail. At one end of the tail, proteins associated with the baseplate recognize and bind to the host. At the other end, a connector or "neck" forms the interface between the tail and the head. The neck consists of several specialized proteins with specific roles in DNA packaging, phage assembly, and DNA ejection. Using cryo-electron microscopy and three-dimensional reconstruction, we have determined the high-resolution structure of the neck section of SaPI1 virions made in the presence of phage 80α, including the dodecameric portal (80α gene product (gp) 42) and head-tail-connector (gp49) proteins, the hexameric head-tail joining (gp50) and tail terminator (gp52) proteins, and the major tail protein (gp53) itself. We were also able to resolve the DNA, the tail completion protein (gp51) and the tape measure protein (gp56) inside the tail. This is the first detailed structural description of these features in a bacteriophage, providing insights into the assembly and infection process in this important group of MGEs and their helper bacteriophages.
History
DepositionJan 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 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
G: Head-tail connector protein
H: Head-tail connector protein
I: adaptor
J: DUF3168 domain-containing protein
K: Major tail protein
L: Major tail protein
M: Tape measure protein
N: Tape measure protein
O: Tape measure protein
P: HK97 gp10 family phage protein
Q: DNA, 5'-3'
R: DNA, 3'-5'
S: Head-tail connector protein
T: Head-tail connector protein
U: adaptor
V: DUF3168 domain-containing protein
W: Major tail protein
X: Major tail protein
Y: Head-tail connector protein
Z: Head-tail connector protein
a: adaptor
b: DUF3168 domain-containing protein
c: Major tail protein
d: Major tail protein
e: Head-tail connector protein
f: Head-tail connector protein
g: adaptor
h: DUF3168 domain-containing protein
i: Major tail protein
j: Major tail protein
k: Head-tail connector protein
l: Head-tail connector protein
m: adaptor
n: DUF3168 domain-containing protein
o: Major tail protein
p: Major tail protein


Theoretical massNumber of molelcules
Total (without water)28,046,57942
Polymers28,046,57942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 40 molecules ABGHSTYZefklCIUagmDJVbhnEFKLWX...

#1: Protein
Head-tail connector protein


Mass: 12809.583 Da / Num. of mol.: 12 / 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.: 6 / 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.: 6 / 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.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: UniProt: A4ZFB9
#5: Protein Tape measure protein


Mass: 125891.977 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: UniProt: A4ZFC2
#6: Protein HK97 gp10 family phage protein


Mass: 13482.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: UniProt: A0AA96SGB5

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DNA chain , 2 types, 2 molecules QR

#7: DNA chain DNA, 5'-3'


Mass: 13596138.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: GenBank: 148717842
#8: DNA chain DNA, 3'-5'


Mass: 13487673.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 80alpha (virus) / References: GenBank: 148717842

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Details

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 / 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: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35724 / Symmetry type: POINT

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