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- EMDB-7030: Staphylococcus aureus phage 80alpha procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-7030
TitleStaphylococcus aureus phage 80alpha procapsid
Map dataCapsid protein and C-terminal part of scaffolding protein in the Staphylococcus aureus phage 80alpha procapsid: clipped map used for model building and refinement in Coot and REFMAC
Sample
  • Virus: Staphylococcus phage 80alpha (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: Scaffold protein
Keywordsmajor capsid protein / HK97-like fold / scaffolding protein / procapsid / VIRUS
Function / homology
Function and homology information


viral scaffold / viral capsid / symbiont-mediated suppression of host innate immune response
Similarity search - Function
Protein of unknown function DUF4355 / Capsid assembly scaffolding protein Gp46 / : / Phage capsid / Phage capsid family
Similarity search - Domain/homology
Capsid assembly scaffolding protein / Major capsid protein
Similarity search - Component
Biological speciesStaphylococcus phage 80alpha (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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)R01AI083255 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 15, 2017-
Header (metadata) releaseOct 11, 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: 0.00705
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00705
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6b0x
  • Surface level: 0.00705
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7030.png

Downloads & links

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Map

FileDownload / File: emd_7030.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid protein and C-terminal part of scaffolding protein in the Staphylococcus aureus phage 80alpha procapsid: clipped map used for model building and refinement in Coot and REFMAC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 240 pix.
= 290.4 Å		1.21 Å/pix.
x 480 pix.
= 580.8 Å		1.21 Å/pix.
x 480 pix.
= 580.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00705 / Movie #1: 0.00705
Minimum - Maximum-0.014348721 - 0.02552154
Average (Standard dev.)0.00015101467 (±0.0023900704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480240
Spacing480480240
CellA: 580.80005 Å / B: 580.80005 Å / C: 290.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z480480240
origin x/y/z0.0000.0000.000
length x/y/z580.800580.800290.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480240
D min/max/mean-0.0140.0260.000

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Supplemental data

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

Fileemd_7030_additional.map
AnnotationCapsid protein and C-terminal part of scaffolding protein in the Staphylococcus aureus phage 80alpha procapsid: final map sharpened with a B-factor of 300 to 6 Angstrom resolution (cutoff at 3 Angstrom)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Staphylococcus phage 80alpha

EntireName: Staphylococcus phage 80alpha (virus)
Components
  • Virus: Staphylococcus phage 80alpha (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: Scaffold 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: 25.27 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: 7 / 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: Scaffold protein

MacromoleculeName: Scaffold protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 23.410941 KDa
Recombinant expressionOrganism: Staphylococcus aureus (bacteria)
SequenceString: MEENKLKFNL QFFADQSDDP DEPGGDGKKG NPDKKENDEG TEITFTPEQQ KKVDEILERR VAHEKKKADE YAKEKAAEAA KEAAKLAKM NKDQKDEYER EQMEKELEQL RSEKQLNEMR SEARKMLSEA EVDSSDEVVN LVVTDTAEQT KSNVEAFSNA V KKAVNEAV ...String:
MEENKLKFNL QFFADQSDDP DEPGGDGKKG NPDKKENDEG TEITFTPEQQ KKVDEILERR VAHEKKKADE YAKEKAAEAA KEAAKLAKM NKDQKDEYER EQMEKELEQL RSEKQLNEMR SEARKMLSEA EVDSSDEVVN LVVTDTAEQT KSNVEAFSNA V KKAVNEAV KVNARQSPLT GGDSFNHSTK NKPQNLAEIA RQKRIIKN

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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10557
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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