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- EMDB-0131: HHIV-2 pentameric vertex complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0131
TitleHHIV-2 pentameric vertex complex
Map data
Sample
  • Complex: HHIV-2 spike complex composed of VP9 and putatively of VP16, VP17 and VP2
Biological speciesHaloarcula hispanica icosahedral virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsSantos-Perez I / Charro D / Gil-Carton D / Azkagorta M / Elortza F / Bamford DH / Oksanen HM / Abrescia NGA
Funding support Spain, Finland, 4 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-64541-R Spain
Academy of Finland1306833, 255342,256518,283072 Finland
Spanish Ministry of Economy and CompetitivenessSEV-2016-0644 Spain
Other governmentBasque Governament PRE_2016_2_0151 Spain
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
DepositionJul 16, 2018-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateNov 4, 2020-
Current statusNov 4, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0131.png

Downloads & links

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Map

FileDownload / File: emd_0131.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.10049294 - 0.20684582
Average (Standard dev.)-0.0042278017 (±0.007181816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 514.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z514.560514.560514.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1000.207-0.004

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Supplemental data

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Mask #1

Fileemd_0131_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_0131_additional.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_0131_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0131_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_0131_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : HHIV-2 spike complex composed of VP9 and putatively of VP16, VP17...

EntireName: HHIV-2 spike complex composed of VP9 and putatively of VP16, VP17 and VP2
Components
  • Complex: HHIV-2 spike complex composed of VP9 and putatively of VP16, VP17 and VP2

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Supramolecule #1: HHIV-2 spike complex composed of VP9 and putatively of VP16, VP17...

SupramoleculeName: HHIV-2 spike complex composed of VP9 and putatively of VP16, VP17 and VP2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2

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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
20.0 mMC4H11NO3Tris-HClTris
20.0 mMMgCl2Magnessium clorhide
10.0 mMCaCl2Calcium Clorhide
0.5 MNaClSodium chlorideSodium Clorhide
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 137352
Details: number of subboxed spike complexes extracted in silico from 2D cryo-images projections of the whole virion.
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER / Details: Reconstructed map
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Details: the two halves were extracted randomly / Number images used: 58176
FSC plot (resolution estimation)

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