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- EMDB-5600: Penicillium Chrysogenum Virus (PcV) capsid structure -

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Basic information

Entry
Database: EMDB / ID: EMD-5600
TitlePenicillium Chrysogenum Virus (PcV) capsid structure
Map dataReconstruction of Penicillium Chrysogenum Virus at near-atomic resolution
Sample
  • Sample: Penicillium Chrysogenum Virus
  • Virus: Penicillium chrysogenum virus
Keywordsdouble-stranded RNA / fungal virus / viral structure / T=1 virus / duplicated helical fold
Function / homology: / : / Fungal virus Capsid protein, N-terminal domain / Fungal virus Capsid protein, C-terminal domain / T=1 icosahedral viral capsid / Capsid protein
Function and homology information
Biological speciesPenicillium chrysogenum virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLuque D / Gomez-Blanco J / Garriga D / Brilot A / Gonzalez JM / Havens WH / Carrascosa JL / Trus BL / Verdaguer N / Grigorieff N ...Luque D / Gomez-Blanco J / Garriga D / Brilot A / Gonzalez JM / Havens WH / Carrascosa JL / Trus BL / Verdaguer N / Grigorieff N / Ghabrial SA / Caston JR
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage.
Authors: Daniel Luque / Josué Gómez-Blanco / Damiá Garriga / Axel F Brilot / José M González / Wendy M Havens / José L Carrascosa / Benes L Trus / Nuria Verdaguer / Said A Ghabrial / José R Castón /
Abstract: Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of ...Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of viral classes or lineages that can be grouped by capsid protein (CP) folds. Here, we report that the CP structure of the fungal dsRNA Penicillium chrysogenum virus (PcV) shows the progenitor fold of the dsRNA virus lineage and suggests a relationship between lineages. Cryo-EM structure at near-atomic resolution showed that the 982-aa PcV CP is formed by a repeated α-helical core, indicative of gene duplication despite lack of sequence similarity between the two halves. Superimposition of secondary structure elements identified a single "hotspot" at which variation is introduced by insertion of peptide segments. Structural comparison of PcV and other distantly related dsRNA viruses detected preferential insertion sites at which the complexity of the conserved α-helical core, made up of ancestral structural motifs that have acted as a skeleton, might have increased, leading to evolution of the highly varied current structures. Analyses of structural motifs only apparent after systematic structural comparisons indicated that the hallmark fold preserved in the dsRNA virus lineage shares a long (spinal) α-helix tangential to the capsid surface with the head-tailed phage and herpesvirus viral lineage.
History
DepositionMar 8, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseMay 14, 2014-
UpdateJun 25, 2014-
Current statusJun 25, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j3i
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j3i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5600.png

Downloads & links

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Map

FileDownload / File: emd_5600.map.gz / Format: CCP4 / Size: 231.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Penicillium Chrysogenum Virus at near-atomic resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 396 pix.
= 487.08 Å		1.23 Å/pix.
x 396 pix.
= 487.08 Å		1.23 Å/pix.
x 396 pix.
= 487.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.05330282 - 0.04782657
Average (Standard dev.)0.00010026 (±0.00569365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-198-198-198
Dimensions396396396
Spacing396396396
CellA=B=C: 487.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z396396396
origin x/y/z0.0000.0000.000
length x/y/z487.080487.080487.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-198-198-198
NC/NR/NS396396396
D min/max/mean-0.0530.0480.000

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Supplemental data

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Sample components

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Entire : Penicillium Chrysogenum Virus

EntireName: Penicillium Chrysogenum Virus
Components
  • Sample: Penicillium Chrysogenum Virus
  • Virus: Penicillium chrysogenum virus

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Supramolecule #1000: Penicillium Chrysogenum Virus

SupramoleculeName: Penicillium Chrysogenum Virus / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightTheoretical: 6.5 MDa

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Supramolecule #1: Penicillium chrysogenum virus

SupramoleculeName: Penicillium chrysogenum virus / type: virus / ID: 1 / NCBI-ID: 158372 / Sci species name: Penicillium chrysogenum virus / Sci species strain: from ATCC 9480 host / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Penicillium chrysogenum (fungus) / Strain: ATCC 9480 / synonym: FUNGI
Molecular weightTheoretical: 6.5 MDa
Virus shellShell ID: 1 / Name: CP / Diameter: 400 Å / T number (triangulation number): 1

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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: 7.8 / Details: 50 mM Tris-HCl , 150 mM NaCl, 5 mM EDTA
GridDetails: C flat CF 1/2 4C grids
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II
Method: Samples were applied to grids, blotted 7 seconds, and plunged into liquid ethane.

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Electron microscopy

MicroscopeFEI TECNAI F30
DateFeb 23, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 650 / Average electron dose: 25 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56910 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 58333
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping & amplitude
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Xmipp / Number images used: 27566

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