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- EMDB-7333: Staphylococcus aureus phage 80alpha-derived SaPI1 mature capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-7333
TitleStaphylococcus aureus phage 80alpha-derived SaPI1 mature capsid
Map dataStaphylococcus aureus phage 80alpha-derived SaPI1 mature capsid. Sharpened map used for model fitting and refinement. Map sharpened with bsoft by application of inverse Bfactor = 800.
Sample
  • Virus: Staphylococcus phage 80alpha (virus)
    • Protein or peptide: Major head protein
Keywordsmajor capsid protein / HK97-like fold / mature capsid / VIRUS
Function / homology: / Phage capsid / Phage capsid family / viral capsid / Major capsid protein
Function and homology information
Biological speciesStaphylococcus virus 80alpha / Staphylococcus phage 80alpha (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsDokland T
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: Viruses / Year: 2017
Title: Cleavage and Structural Transitions during Maturation of Staphylococcus aureus Bacteriophage 80α and SaPI1 Capsids.
Authors: James L Kizziah / Keith A Manning / Altaira D Dearborn / Erin A Wall / Laura Klenow / Rosanne L L Hill / Michael S Spilman / Scott M Stagg / Gail E Christie / Terje Dokland /
Abstract: In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of ...In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of the major capsid protein (CP) and other capsid-associated proteins, including the scaffolding protein (SP) that serves as a chaperone for the assembly process. bacteriophage 80α is capable of high frequency mobilization of mobile genetic elements called pathogenicity islands (SaPIs), such as SaPI1. SaPI1 redirects the assembly pathway of 80α to form capsids that are smaller than those normally made by the phage alone. Both CP and SP of 80α are N-terminally processed by a host-encoded protease, Prp. We have analyzed phage mutants that express pre-cleaved or uncleavable versions of CP or SP, and show that the N-terminal sequence in SP is absolutely required for assembly, but does not need to be cleaved in order to produce viable capsids. Mutants with pre-cleaved or uncleavable CP display normal viability. We have used cryo-EM to solve the structures of mature capsids from an 80α mutant expressing uncleavable CP, and from wildtype SaPI1. Comparisons with structures of 80α and SaPI1 procapsids show that capsid maturation involves major conformational changes in CP, consistent with a release of the CP N-arm by SP. The hexamers reorganize during maturation to accommodate the different environments in the 80α and SaPI1 capsids.
History
DepositionJan 5, 2018-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
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: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6c22
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6c22
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7333.png

Downloads & links

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Map

FileDownload / File: emd_7333.map.gz / Format: CCP4 / Size: 92.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStaphylococcus aureus phage 80alpha-derived SaPI1 mature capsid. Sharpened map used for model fitting and refinement. Map sharpened with bsoft by application of inverse Bfactor = 800.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 289 pix.
= 591.872 Å		2.05 Å/pix.
x 289 pix.
= 591.872 Å		2.05 Å/pix.
x 289 pix.
= 591.872 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-6.673943 - 10.581618000000001
Average (Standard dev.)-0.000000003075934 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions289289289
Spacing289289289
CellA=B=C: 591.872 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0482.0482.048
M x/y/z289289289
origin x/y/z0.0000.0000.000
length x/y/z591.872591.872591.872
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS289289289
D min/max/mean-6.67410.582-0.000

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Supplemental data

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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

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Supramolecule #1: Staphylococcus phage 80alpha

SupramoleculeName: Staphylococcus phage 80alpha / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 53369 / Sci species name: Staphylococcus phage 80alpha / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 8.83 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 460.0 Å / T number (triangulation number): 4

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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 virus 80alpha
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: KODAK SO-163 FILM / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 62000
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6471
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM (ver. 4.01) / Number images used: 6471
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: Auto3DEM (ver. 4.01)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Auto3DEM (ver. 4.01)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6c22:
Capsid protein in the Staphylococcus aureus phage 80alpha-derived SaPI1 mature capsid

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