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- EMDB-1624: Three-dimensional structure of the recombinant, virus-like partic... -

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Basic information

Entry
Database: EMDB / ID: EMD-1624
TitleThree-dimensional structure of the recombinant, virus-like particle of Penaeus stylirostris densovirus (PstDNV) or infectious hypodermal and hematopoietic necrosis virus (IHHNV)
Map dataPenaeus stylirostris densovirus (PstDNV) or infectious hypodermal and hematopoietic necrosis virus (IHHNV)
Sample
  • Sample: recombinant, virus-like particle of Penaeus stylirostris densovirus (PstDNV) or infectious hypodermal and hematopoietic necrosis virus (IHHNV)
  • Virus: Infectious hypodermal and hematopoietic necrosis virus
Keywordsvirus-like particle / VLP / parvovirus / Densovirinae / shrimp pathogen / protein capsid
Biological speciesInfectious hypodermal and hematopoietic necrosis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.17 Å
AuthorsKaufmann B / Bowman VD / Li Y / Szelei J / Tijssen P / Rossmann MG
CitationJournal: J Virol / Year: 2010
Title: Structure of Penaeus stylirostris densovirus, a shrimp pathogen.
Authors: Bärbel Kaufmann / Valorie D Bowman / Yi Li / Jozsef Szelei / Peter J Waddell / Peter Tijssen / Michael G Rossmann /
Abstract: Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only ...Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5-kDa coat protein, the smallest parvoviral capsid protein reported thus far, was determined to 2.5-Å resolution by X-ray crystallography. The structure represents the first near-atomic resolution structure within the genus Brevidensovirus. The capsid protein has a β-barrel "jelly roll" motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the PstDNV coat protein adopts a "domain-swapped" conformation relative to its twofold-related neighbor similar to the insect parvovirus Galleria mellonella densovirus (GmDNV) but in stark contrast to vertebrate parvoviruses. However, most of the surface loops have little structural resemblance to any of the known parvoviral capsid proteins.
History
DepositionJun 19, 2009-
Header (metadata) releaseJun 19, 2009-
Map releaseNov 5, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1624_EMD-162...

Downloads & links

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Map

FileDownload / File: emd_1624.map.gz / Format: CCP4 / Size: 52.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPenaeus stylirostris densovirus (PstDNV) or infectious hypodermal and hematopoietic necrosis virus (IHHNV)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 241 pix.
= 358.849 Å		1.49 Å/pix.
x 241 pix.
= 358.849 Å		1.49 Å/pix.
x 241 pix.
= 358.849 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.489 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-11.04978371 - 13.950583460000001
Average (Standard dev.)0.10299776 (±2.20425153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions241241241
Spacing241241241
CellA=B=C: 358.849 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4891.4891.489
M x/y/z241241241
origin x/y/z0.0000.0000.000
length x/y/z358.849358.849358.849
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS241241241
D min/max/mean-11.05013.9510.103

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Supplemental data

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Sample components

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Entire : recombinant, virus-like particle of Penaeus stylirostris densovir...

EntireName: recombinant, virus-like particle of Penaeus stylirostris densovirus (PstDNV) or infectious hypodermal and hematopoietic necrosis virus (IHHNV)
Components
  • Sample: recombinant, virus-like particle of Penaeus stylirostris densovirus (PstDNV) or infectious hypodermal and hematopoietic necrosis virus (IHHNV)
  • Virus: Infectious hypodermal and hematopoietic necrosis virus

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Supramolecule #1000: recombinant, virus-like particle of Penaeus stylirostris densovir...

SupramoleculeName: recombinant, virus-like particle of Penaeus stylirostris densovirus (PstDNV) or infectious hypodermal and hematopoietic necrosis virus (IHHNV)
type: sample / ID: 1000
Details: virus-like particles (VLP) self-assembled 60 copies of the recombinant 37.5-kD viral coat protein only
Oligomeric state: 60 viral coat protein subunits form T1 icosahedral protein shell
Number unique components: 1
Molecular weightTheoretical: 2.25 MDa

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Supramolecule #1: Infectious hypodermal and hematopoietic necrosis virus

SupramoleculeName: Infectious hypodermal and hematopoietic necrosis virus
type: virus / ID: 1 / Name.synonym: Penaeus stylirostris densovirus (PstDNV)
Details: Virus-like particles (VLP) self-assembled from 60 monomers of the recombinant 37.5-kD viral coat protein
NCBI-ID: 111792
Sci species name: Infectious hypodermal and hematopoietic necrosis virus
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Penaeus stylirostris densovirus (PstDNV)
Host (natural)Organism: Litopenaeus stylirostris (blue shrimp) / synonym: INVERTEBRATES
Molecular weightTheoretical: 2.25 MDa
Virus shellShell ID: 1 / Diameter: 225 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

Concentration1. mg/mL
BufferpH: 7.5 / Details: 10mM Tris-HCl, 100mM NaCl, 1mM MgCl2, 1mM CaCl2
GridDetails: Holey carbon 400 mesh copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Guillotine-style plunge freezeing device
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.241 µm / Nominal defocus min: 1.362 µm / Nominal magnification: 45000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: -0
TemperatureAverage: 98 K
Alignment procedureLegacy - Astigmatism: live FFT at 200K mag
Detailslow dose imaging
DateSep 7, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 9 / Average electron dose: 18.41 e/Å2 / Od range: 1.24 / Bits/pixel: 8
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.17 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM
Details: final map includes data to 6.1 Ang resolution (fsc 0.2 cut-off)
Number images used: 9009
DetailsThe particles were selected using an automatic selection program. Selection of particles was subsequently refined interactively at the computer terminal.

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