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- EMDB-22331: SPN3US phage empty capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-22331
TitleSPN3US phage empty capsid
Map dataSPN3US phage empty capsid
Sample
  • Virus: Salmonella phage SPN3US (virus)
Biological speciesSalmonella phage SPN3US (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsHeymann JB / Wang B / Newcomb WW / Wu W / Winkler DC / Cheng N / Reilly ER / Hsia R-C / Thomas JA / Steven AC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)UA5GM126533 United States
CitationJournal: Viruses / Year: 2020
Title: The Mottled Capsid of the Giant Phage SPN3US, a Likely Maturation Intermediate with a Novel Internal Shell.
Authors: J Bernard Heymann / Bing Wang / William W Newcomb / Weimin Wu / Dennis C Winkler / Naiqian Cheng / Erin R Reilly / Ru-Ching Hsia / Julie A Thomas / Alasdair C Steven /
Abstract: "Giant" phages have genomes of >200 kbp, confined in correspondingly large capsids whose assembly and maturation are still poorly understood. Nevertheless, the first assembly product is likely to be, ..."Giant" phages have genomes of >200 kbp, confined in correspondingly large capsids whose assembly and maturation are still poorly understood. Nevertheless, the first assembly product is likely to be, as in other tailed phages, a procapsid that subsequently matures and packages the DNA. The associated transformations include the cleavage of many proteins by the phage-encoded protease, as well as the thinning and angularization of the capsid. We exploited an amber mutation in the viral protease gene of the giant phage SPN3US, which leads to the accumulation of a population of capsids with distinctive properties. Cryo-electron micrographs reveal patterns of internal density different from those of the DNA-filled heads of virions, leading us to call them "mottled capsids". Reconstructions show an outer shell with T = 27 symmetry, an embellishment of the HK97 prototype composed of the major capsid protein, gp75, which is similar to some other giant viruses. The mottled capsid has a T = 1 inner icosahedral shell that is a complex network of loosely connected densities composed mainly of the ejection proteins gp53 and gp54. Segmentation of this inner shell indicated that a number of densities (~12 per asymmetric unit) adopt a "twisted hook" conformation. Large patches of a proteinaceous tetragonal lattice with a 67 Å repeat were also present in the cell lysate. The unexpected nature of these novel inner shell and lattice structures poses questions as to their functions in virion assembly.
History
DepositionJul 20, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22331.png

Downloads & links

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Map

FileDownload / File: emd_22331.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSPN3US phage empty capsid
Voxel sizeX=Y=Z: 3.512 Å
Density
Contour LevelBy AUTHOR: 3 / Movie #1: 3
Minimum - Maximum-7.9673204 - 12.287279
Average (Standard dev.)0.0000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 1756.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.5123.5123.512
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z1756.0001756.0001756.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS500500500
D min/max/mean-7.96712.2870.000

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Supplemental data

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Mask #1

Fileemd_22331_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 1

Fileemd_22331_half_map_1.map
Annotationhalf-volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 2

Fileemd_22331_half_map_2.map
Annotationhalf-volume 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Salmonella phage SPN3US

EntireName: Salmonella phage SPN3US (virus)
Components
  • Virus: Salmonella phage SPN3US (virus)

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Supramolecule #1: Salmonella phage SPN3US

SupramoleculeName: Salmonella phage SPN3US / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1090134 / Sci species name: Salmonella phage SPN3US / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica (bacteria)
Host systemOrganism: Salmonella enterica (bacteria) / Recombinant strain: Typhimurium T9079
Molecular weightTheoretical: 195 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1460.0 Å / T number (triangulation number): 27

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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

Concentration2 mg/mL
BufferpH: 8
GridModel: Homemade / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY
Details: Grids were from Ted Pella; Lacey carbon with a thin, continuous carbon film
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
DetailsEmpty capsid isolated from a cell lysate and purified using sucrose density gradient centrifugation.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.49 µm / Calibrated magnification: 28400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 1178 / Average exposure time: 15.0 sec. / Average electron dose: 138.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8633
CTF correctionSoftware - Name: Bsoft (ver. 2.0.5)
Startup modelType of model: OTHER
Details: Derived from icosahedral symmetry using the maximum power algorithm in bmaxpow.
Initial angle assignmentType: OTHER / Software - Name: Bsoft (ver. 2.0.5)
Details: Based on icosahedral symmetry using the maximum power algorithm in bmaxpow, followed by borient.
Final angle assignmentType: PROJECTION MATCHING / Projection matching processing - Merit function: FRC
Projection matching processing - Angular sampling: 0.1 degrees
Software - Name: Bsoft (ver. 2.0.5)
Details: Refinement of angular assignments with a contracting grid search to an arbitrary accuracy.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Bsoft (ver. 2.0.5) / Number images used: 1000
FSC plot (resolution estimation)

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