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- EMDB-7035: Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-7035
TitleStaphylococcus aureus pathogenicity island 1 80alpha-derived procapsid
Map dataCapsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid: clipped map used for model building and refinement in Coot and REFMAC.
SampleLysogenic 80alpha with small terminase != Staphylococcus phage 80alpha

Lysogenic 80alpha with small terminase

  • Virus: Staphylococcus phage 80alpha (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: Capsid morphogenesis B protein
Keywordsmajor capsid protein / HK97-like fold / scaffolding protein / procapsid / VIRUS
Function / homologyPathogenicity island protein gp6, Staphylococcus / Pathogenicity island protein gp6 superfamily / Pathogenicity island protein gp6 in Staphylococcus / Phage capsid / Phage capsid family / molecular adaptor activity / Major capsid protein / Hypothetical mobile element-associated protein
Function and homology information
Biological speciesStaphylococcus phage 80alpha (virus) / Staphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKizziah JL / Dearborn AD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: Elife / Year: 2017
Title: Competing scaffolding proteins determine capsid size during mobilization of pathogenicity islands.
Authors: Altaira D Dearborn / Erin A Wall / James L Kizziah / Laura Klenow / Laura K Parker / Keith A Manning / Michael S Spilman / John M Spear / Gail E Christie / Terje Dokland /
Abstract: pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the ... pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the helper's assembly pathway to form small capsids that can only accommodate the smaller SaPI1 genome, but not a complete phage genome. SaPI1 encodes two proteins, CpmA and CpmB, that are responsible for this size redirection. We have determined the structures of the 80α and SaPI1 procapsids to near-atomic resolution by cryo-electron microscopy, and show that CpmB competes with the 80α scaffolding protein (SP) for a binding site on the capsid protein (CP), and works by altering the angle between capsomers. We probed these interactions genetically and identified second-site suppressors of lethal mutations in SP. Our structures show, for the first time, the detailed interactions between SP and CP in a bacteriophage, providing unique insights into macromolecular assembly processes.
History
DepositionSep 19, 2017-
Header (metadata) releaseOct 4, 2017-
Map releaseOct 18, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.75
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.75
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6b23
  • Surface level: 5.75
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7035.png

Downloads & links

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Map

FileDownload / File: emd_7035.map.gz / Format: CCP4 / Size: 171.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid: clipped map used for model building and refinement in Coot and REFMAC.
Voxel sizeX=Y=Z: 1.212 Å
Density
Contour LevelBy AUTHOR: 5.75 / Movie #1: 5.75
Minimum - Maximum-17.282436000000001 - 26.090025000000001
Average (Standard dev.)0.024060378 (±2.1046886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448224
Spacing448448224
CellA: 542.976 Å / B: 542.976 Å / C: 271.488 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2121.2121.212
M x/y/z448448224
origin x/y/z0.0000.0000.000
length x/y/z542.976542.976271.488
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448224
D min/max/mean-17.28226.0900.024

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Supplemental data

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Additional map: Capsid protein and C-terminal part of CpmB protein...

Fileemd_7035_additional.map
AnnotationCapsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid: final map from reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lysogenic 80alpha with small terminase

EntireName: Lysogenic 80alpha with small terminase
Components
  • Virus: Staphylococcus phage 80alpha (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: Capsid morphogenesis B protein

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Supramolecule #1: Staphylococcus phage 80alpha

SupramoleculeName: Staphylococcus phage 80alpha / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Lysogenic 80alpha with small terminase gene deletion
NCBI-ID: 53369 / Sci species name: Staphylococcus phage 80alpha / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 10.81 MDa
Virus shellShell ID: 1 / Name: Procapsid / Diameter: 546.0 Å / T number (triangulation number): 7

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Macromolecule #1: Major head protein

MacromoleculeName: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 36.846883 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
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

UniProtKB: Major capsid protein

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Macromolecule #2: Capsid morphogenesis B protein

MacromoleculeName: Capsid morphogenesis B protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 8.281234 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
SequenceString:
METKYELNNT KKVANAFGLN EEDTNLLINA VDLDIKNNMQ EISSELQQSE QSKQKQYGTT LQNLAKQNRI IK

UniProtKB: Hypothetical mobile element-associated 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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14087
FSC plot (resolution estimation)

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