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- EMDB-1608: NwV assembly and maturation -

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Basic information

Entry
Database: EMDB / ID: EMD-1608
TitleNwV assembly and maturation
Map dataMap of NwV VLP capsid
Sample
  • Sample: NwV
  • Virus: Nudaurelia capensis omega virus
KeywordsAssembly / maturation
Biological speciesNudaurelia capensis omega virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsTang J / Lee KK / Bothner B / Baker TS / Yeager M / Johnson JE
CitationJournal: J Mol Biol / Year: 2009
Title: Dynamics and stability in maturation of a T=4 virus.
Authors: Jinghua Tang / Kelly K Lee / Brian Bothner / Timothy S Baker / Mark Yeager / John E Johnson /
Abstract: Nudaurelia capensis omega virus is a T=4, icosahedral virus with a bipartite, positive-sense RNA genome. Expression of the coat protein gene in a baculovirus system was previously shown to result in ...Nudaurelia capensis omega virus is a T=4, icosahedral virus with a bipartite, positive-sense RNA genome. Expression of the coat protein gene in a baculovirus system was previously shown to result in the formation of procapsids when purified at pH 7.6. Procapsids are round, porous particles (480 A diameter) and have T=4 quasi-symmetry. Reduction of pH from 7.6 to 5.0 resulted in virus-like particles (VLP(5.0)) that are morphologically identical with authentic virions, with an icosahedral-shaped capsid and a maximum dimension of 410 A. VLP(5.0) undergoes a maturation cleavage between residues N570 and F571, creating the covalently independent gamma peptide (residues 571-641) that remains associated with the particle. This cleavage also occurs in authentic virions, and in each case, it renders the morphological change irreversible (i.e., capsids do not expand when the pH is raised back to 7.6). However, a non-cleavable mutant, N570T, undergoes the transition reversibly (NT(7.6)<-->NT(5.0)). We used electron cryo-microscopy and three-dimensional image reconstruction to study the icosahedral structures of NT(7.6), NT(5.0), and VLP(5.0) at about 8, 6, and 6 A resolution, respectively. We employed the 2. 8-A X-ray model of the mature virus, determined at pH 7.0 (XR(7.0)), to establish (1) how and why procapsid and capsid structures differ, (2) why lowering pH drives the transition, and (3) why the non-cleaving NT(5.0) is reversible. We show that procapsid assembly minimizes the differences in quaternary interactions in the particle. The two classes of 2-fold contacts in the T=4 surface lattice are virtually identical, both mediated by similarly positioned but dynamic gamma peptides. Furthermore, quasi and icosahedral 3-fold interactions are indistinguishable. Maturation results from neutralizing the repulsive negative charge at subunit interfaces with significant differentiation of quaternary interactions (one 2-fold becomes flat, mediated by a gamma peptide, while the other is bent with the gamma peptide disordered) and dramatic stabilization of the particle. The gamma peptide at the flat contact remains dynamic when cleavage cannot occur (NT(5.0)) but becomes totally immobilized by noncovalent interactions after cleavage (VLP(5.0)).
History
DepositionMar 20, 2009-
Header (metadata) releaseApr 15, 2009-
Map releaseNov 16, 2010-
UpdateMay 6, 2015-
Current statusMay 6, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-1608.gif

Downloads & links

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Map

FileDownload / File: emd_1608.map.gz / Format: CCP4 / Size: 43 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of NwV VLP capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.74 Å/pix.
x 226 pix.
= 452.1 Å		2.74 Å/pix.
x 226 pix.
= 452.1 Å		2.74 Å/pix.
x 226 pix.
= 452.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-6.5527 - 11.179600000000001
Average (Standard dev.)-0.00000000416961 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-113-113-113
Dimensions226226226
Spacing226226226
CellA=B=C: 452.1 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.742.742.74
M x/y/z165165165
origin x/y/z0.0000.0000.000
length x/y/z452.100452.100452.100
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-113-113-113
NC/NR/NS226226226
D min/max/mean-6.55311.180-0.000

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Supplemental data

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Sample components

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Entire : NwV

EntireName: NwV
Components
  • Sample: NwV
  • Virus: Nudaurelia capensis omega virus

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Supramolecule #1000: NwV

SupramoleculeName: NwV / type: sample / ID: 1000 / Details: Purified / Number unique components: 1

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Supramolecule #1: Nudaurelia capensis omega virus

SupramoleculeName: Nudaurelia capensis omega virus / type: virus / ID: 1 / Name.synonym: NwV / NCBI-ID: 12541 / Sci species name: Nudaurelia capensis omega virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: NwV
Host (natural)Organism: Lepidoptera (butterflies and moths) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 410 Å / T number (triangulation number): 4

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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 mg/mL
BufferpH: 5
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each image
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem

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Atomic model buiding 1

Initial modelPDB ID:

1ohf

RefinementSpace: REAL

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