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- EMDB-43147: SaPI1 portal-capsid interface in mature capsids with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-43147
TitleSaPI1 portal-capsid interface in mature capsids with DNA
Map data
Sample
  • Virus: Dubowvirus dv80alpha
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein
Keywordscapsid / phage / sapi / portal / STRUCTURAL PROTEIN
Biological speciesDubowvirus dv80alpha
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKizziah JL / Mukherjee A / Dokland T
Funding support United States, 4 items
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, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43147.png

Downloads & links

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Map

FileDownload / File: emd_43147.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.33 Å
Density
Contour LevelBy AUTHOR: 0.645
Minimum - Maximum-1.503183 - 2.499361
Average (Standard dev.)0.025912873 (±0.16134445)
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_43147_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: C12 symmetry averaged map resampled to main map...

Fileemd_43147_additional_1.map
AnnotationC12 symmetry averaged map resampled to main map used to constrain portal protein models in ISOLDE
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: C5 symmetry averaged map resampled to main map...

Fileemd_43147_additional_2.map
AnnotationC5 symmetry averaged map resampled to main map used to constrain capsid protein models in ISOLDE
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_43147_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_43147_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Dubowvirus dv80alpha

EntireName: Dubowvirus dv80alpha
Components
  • Virus: Dubowvirus dv80alpha
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein

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Supramolecule #1: Dubowvirus dv80alpha

SupramoleculeName: Dubowvirus dv80alpha / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 53369 / Sci species name: Dubowvirus dv80alpha / Virus type: SATELLITE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Dubowvirus dv80alpha
Molecular weightTheoretical: 36.846883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEQTQKLKLN LQHFASNNVK PQVFNPDNVM MHEKKDGTLM NEFTTPILQE VMENSKIMQL GKYEPMEGTE KKFTFWADKP GAYWVGEGQ KIETSKATWV NATMRAFKLG VILPVTKEFL NYTYSQFFEE MKPMIAEAFY KKFDEAGILN QGNNPFGKSI A QSIEKTNK ...String:
MEQTQKLKLN LQHFASNNVK PQVFNPDNVM MHEKKDGTLM NEFTTPILQE VMENSKIMQL GKYEPMEGTE KKFTFWADKP GAYWVGEGQ KIETSKATWV NATMRAFKLG VILPVTKEFL NYTYSQFFEE MKPMIAEAFY KKFDEAGILN QGNNPFGKSI A QSIEKTNK VIKGDFTQDN IIDLEALLED DELEANAFIS KTQNRSLLRK IVDPETKERI YDRNSDSLDG LPVVNLKSSN LK RGELITG DFDKLIYGIP QLIEYKIDET AQLSTVKNED GTPVNLFEQD MVALRATMHV ALHIADDKAF AKLVPADKRT DSV PGEV

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Macromolecule #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Dubowvirus dv80alpha
Molecular weightTheoretical: 59.55182 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLKVNEFETD TDLRGNINYL FNDEANVVYT YDGTESDLLQ NVNEVSKYIE HHMDYQRPRL KVLSDYYEGK TKNLVELTRR KEEYMADNR VAHDYASYIS DFINGYFLGN PIQYQDDDKD VLEAIEAFND LNDVESHNRS LGLDLSIYGK AYELMIRNQD D ETRLYKSD ...String:
MLKVNEFETD TDLRGNINYL FNDEANVVYT YDGTESDLLQ NVNEVSKYIE HHMDYQRPRL KVLSDYYEGK TKNLVELTRR KEEYMADNR VAHDYASYIS DFINGYFLGN PIQYQDDDKD VLEAIEAFND LNDVESHNRS LGLDLSIYGK AYELMIRNQD D ETRLYKSD AMSTFIIYDN TVERNSIAGV RYLRTKPIDK TDEDEVFTVD LFTSHGVYRY LTNRTNGLKL TPRENSFESH SF ERMPITE FSNNERRKGD YEKVITLIDL YDNAESDTAN YMSDLNDAML LIKGNLNLDP VEVRKQKEAN VLFLEPTVYV DAE GRETEG SVDGGYIYKQ YDVQGTEAYK DRLNSDIHMF TNTPNMKDDN FSGTQSGEAM KYKLFGLEQR TKTKEGLFTK GLRR RAKLL ETILKNTRSI DANKDFNTVR YVYNRNLPKS LIEELKAYID SGGKISQTTL MSLFSFFQDP ELEVKKIEED EKESI KKAQ KGIYKDPRDI NDDEQDDDTK DTVDKKE

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

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59457
FSC plot (resolution estimation)

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