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- EMDB-0073: Localized reconstructed spike HCIV-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0073
TitleLocalized reconstructed spike HCIV-1
Map data
Sample
  • Virus: Haloarcula californiae ATCC 33799 (Halophile)
Biological speciesHaloarcula californiae ATCC 33799 (Halophile)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsSantos-Perez I / Charro D / Gil-Carton D / Azkargorta M / Elortza F / Bamford DH / Oksanen HM / Abrescia NGA
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for assembly of vertical single β-barrel viruses.
Authors: Isaac Santos-Pérez / Diego Charro / David Gil-Carton / Mikel Azkargorta / Felix Elortza / Dennis H Bamford / Hanna M Oksanen / Nicola G A Abrescia /
Abstract: The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The ...The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs.
History
DepositionJun 22, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseMar 27, 2019-
UpdateApr 3, 2019-
Current statusApr 3, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0073.png

Downloads & links

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Map

FileDownload / File: emd_0073.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.06191935 - 0.14325483
Average (Standard dev.)0.00035233182 (±0.010948072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0620.1430.000

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Supplemental data

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Additional map: local resolution estimation performed using the post-processing-like procedure...

Fileemd_0073_additional.map
Annotationlocal resolution estimation performed using the post-processing-like procedure in RELION 2.1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0073_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_0073_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Haloarcula californiae ATCC 33799

EntireName: Haloarcula californiae ATCC 33799 (Halophile)
Components
  • Virus: Haloarcula californiae ATCC 33799 (Halophile)

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Supramolecule #1: Haloarcula californiae ATCC 33799

SupramoleculeName: Haloarcula californiae ATCC 33799 / type: virus / ID: 1 / Parent: 0 / Details: Haloarcula californiae icosahedral virus - 1 / NCBI-ID: 662475 / Sci species name: Haloarcula californiae ATCC 33799 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Haloarcula californiae ATCC 33799 (Halophile)
Virus shellShell ID: 1 / Diameter: 800.0 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

Concentration1.2 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
1.0 MNaClSodium chlorideSodium Chloride
70.0 mMMgCl2Magnesium Chloride
20.0 mMKClPotasium Chloride
1.0 mMCaCl2Calcium Chloride
50.0 mMC4H11NO3Tris-HClTris
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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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 / Cs: 2.7 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-26 / Number grids imaged: 1 / Number real images: 3218 / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 40968
Details: Particles from Localized Reconstruction cutting 12 vertices of 3414 viruses.
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER
Details: Reconstruction of all vertices imposing C2 symmetry
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 11607
FSC plot (resolution estimation)

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