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- PDB-8vde: SaPI1 portal-capsid interface in mature capsids with DNA -

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Basic information

Entry
Database: PDB / ID: 8vde
TitleSaPI1 portal-capsid interface in mature capsids with DNA
Components
  • Major capsid protein
  • Portal protein
KeywordsSTRUCTURAL PROTEIN / capsid / phage / sapi / portal
Biological speciesDubowvirus dv80alpha
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKizziah, J.L. / Mukherjee, A. / Dokland, T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD024978 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA013148 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI083255 United States
CitationJournal: J Mol Biol / Year: 2024
Title: Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation.
Authors: Amarshi Mukherjee / James L Kizziah / N'Toia C Hawkins / Mohamed O Nasef / Laura K Parker / Terje Dokland /
Abstract: Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often ...Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B1: Major capsid protein
B2: Major capsid protein
B3: Major capsid protein
B4: Major capsid protein
B5: Major capsid protein
C1: Major capsid protein
C2: Major capsid protein
C3: Major capsid protein
C4: Major capsid protein
C5: Major capsid protein
D1: Major capsid protein
D2: Major capsid protein
D3: Major capsid protein
D4: Major capsid protein
D5: Major capsid protein
P1: Portal protein
P2: Portal protein
P3: Portal protein
P4: Portal protein
P5: Portal protein
P6: Portal protein
P7: Portal protein
P8: Portal protein
P9: Portal protein
Q1: Portal protein
Q2: Portal protein
Q3: Portal protein


Theoretical massNumber of molelcules
Total (without water)1,267,32527
Polymers1,267,32527
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Major capsid protein


Mass: 36846.883 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dubowvirus dv80alpha / Production host: Escherichia coli (E. coli)
#2: Protein
Portal protein


Mass: 59551.820 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dubowvirus dv80alpha / Production host: Escherichia coli (E. coli)

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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: Dubowvirus dv80alpha / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Dubowvirus dv80alpha
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: SATELLITE
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: FEI TITAN 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 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59457 / Symmetry type: POINT

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