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- EMDB-4656: Localized reconstruction of archaeal virus SH1 spike calculated w... -

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Basic information

Entry
Database: EMDB / ID: EMD-4656
TitleLocalized reconstruction of archaeal virus SH1 spike calculated with C2 symmetry
Map dataReconstruction of SH1 spike
Sample
  • Virus: Haloarcula hispanica virus SH1
Biological speciesHaloarcula hispanica virus SH1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsDe Colibus L / Ilca SL / Stuart DIS / Huiskonen JT
CitationJournal: Nat Commun / Year: 2019
Title: Assembly of complex viruses exemplified by a halophilic euryarchaeal virus.
Authors: Luigi De Colibus / Elina Roine / Thomas S Walter / Serban L Ilca / Xiangxi Wang / Nan Wang / Alan M Roseman / Dennis Bamford / Juha T Huiskonen / David I Stuart /
Abstract: Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). ...Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). Here, by high-resolution cryo-EM analysis, we show that a class of archaeal viruses possess hetero-hexameric MCPs which mimic the PRD1-adeno lineage trimer. These hetero-hexamers are built from heterodimers and utilise a jigsaw-puzzle system of pegs and holes, and underlying minor capsid proteins, to assemble the capsid laterally from the 5-fold vertices. At these vertices proteins engage inwards with the internal membrane vesicle whilst 2-fold symmetric horn-like structures protrude outwards. The horns are assembled from repeated globular domains attached to a central spine, presumably facilitating multimeric attachment to the cell receptor. Such viruses may represent precursors of the main PRD1-adeno lineage, similarly engaging cell-receptors via 5-fold spikes and using minor proteins to define particle size.
History
DepositionMar 4, 2019-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateApr 10, 2019-
Current statusApr 10, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4656.png

Downloads & links

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Map

FileDownload / File: emd_4656.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of SH1 spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.03672785 - 0.0703131
Average (Standard dev.)-0.0029168467 (±0.0051263953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z405.000405.000405.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0370.070-0.003

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Supplemental data

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Sample components

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Entire : Haloarcula hispanica virus SH1

EntireName: Haloarcula hispanica virus SH1
Components
  • Virus: Haloarcula hispanica virus SH1

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Supramolecule #1: Haloarcula hispanica virus SH1

SupramoleculeName: Haloarcula hispanica virus SH1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 326574 / Sci species name: Haloarcula hispanica virus SH1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1000.0 Å / T number (triangulation number): 28

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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

Concentration15 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 47016
Details: 47016 sub-particles were extracted from 3918 particles (12 from each particle, corresponding to the 12 vertices)
Startup modelType of model: OTHER
Details: Localized reconstruction of the vertex calculated using the angles from the refinement of the entire particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 9866
Initial angle assignmentType: OTHER
Details: Angles calculated using the refinement of the entire particle and location of the five-fold vertex
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1) / Software - details: custom / Details: Local alignment of the spike angles
FSC plot (resolution estimation)

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