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- EMDB-4000: Subtomographic reconstruction of a single VP4 spike from Halorubr... -

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Basic information

Entry
Database: EMDB / ID: EMD-4000
TitleSubtomographic reconstruction of a single VP4 spike from Halorubrum pleomorphic virus 1.
Map dataNone
Sample
  • Virus: Halorubrum pleomorphic virus 1
    • Protein or peptide: VP4
Biological speciesHalorubrum pleomorphic virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsButcher SJ / Liljeroos L / Manole V
CitationJournal: J Virol / Year: 2012
Title: Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea.
Authors: Maija K Pietilä / Nina S Atanasova / Violeta Manole / Lassi Liljeroos / Sarah J Butcher / Hanna M Oksanen / Dennis H Bamford /
Abstract: Our understanding of the third domain of life, Archaea, has greatly increased since its establishment some 20 years ago. The increasing information on archaea has also brought their viruses into the ...Our understanding of the third domain of life, Archaea, has greatly increased since its establishment some 20 years ago. The increasing information on archaea has also brought their viruses into the limelight. Today, about 100 archaeal viruses are known, which is a low number compared to the numbers of characterized bacterial or eukaryotic viruses. Here, we have performed a comparative biological and structural study of seven pleomorphic viruses infecting extremely halophilic archaea. The pleomorphic nature of this novel virion type was established by sedimentation analysis and cryo-electron microscopy. These nonlytic viruses form virions characterized by a lipid vesicle enclosing the genome, without any nucleoproteins. The viral lipids are unselectively acquired from host cell membranes. The virions contain two to three major structural proteins, which either are embedded in the membrane or form spikes distributed randomly on the external membrane surface. Thus, the most important step during virion assembly is most likely the interaction of the membrane proteins with the genome. The interaction can be driven by single-stranded or double-stranded DNA, resulting in the virions having similar architectures but different genome types. Based on our comparative study, these viruses probably form a novel group, which we define as pleolipoviruses.
History
DepositionMay 10, 2016-
Header (metadata) releaseJun 1, 2016-
Map releaseJun 1, 2016-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4000.png

Downloads & links

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Map

FileDownload / File: emd_4000.map.gz / Format: CCP4 / Size: 106.4 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 11.5 Å
Density
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-1.3713543 - 3.4430778
Average (Standard dev.)0.33850947 (±0.31467143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin21134
Dimensions303030
Spacing303030
CellA=B=C: 345.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z11.511.511.5
M x/y/z303030
origin x/y/z0.0000.0000.000
length x/y/z345.000345.000345.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS13214
NC/NR/NS303030
D min/max/mean-1.3713.4430.339

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Supplemental data

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Sample components

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Entire : Halorubrum pleomorphic virus 1

EntireName: Halorubrum pleomorphic virus 1
Components
  • Virus: Halorubrum pleomorphic virus 1
    • Protein or peptide: VP4

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Supramolecule #1: Halorubrum pleomorphic virus 1

SupramoleculeName: Halorubrum pleomorphic virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 634168 / Sci species name: Halorubrum pleomorphic virus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Halorubrum sp. PV6 (archaea)

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Macromolecule #1: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorubrum pleomorphic virus 1
SequenceString: msvnrssiks llmvfmivs s sllapvgg aa adefrtp aas dtspea gecs nlddf imfls vgri nadscs rqa yvdaavq dm kdsdanqt k vdiysaaag vkggsetwaa pydnylndt e siawmkae sa iaqsyse ges kteakv aaka aiady ...String:
msvnrssiks llmvfmivs s sllapvgg aa adefrtp aas dtspea gecs nlddf imfls vgri nadscs rqa yvdaavq dm kdsdanqt k vdiysaaag vkggsetwaa pydnylndt e siawmkae sa iaqsyse ges kteakv aaka aiady yatkq knli eqwnfa naq mftlreq ar medgisrn y vepayrnve ktnspdysla ysnttveks l vdgttvnt tg vsmdvtv qht tvsdva tvss gpvra gkynn qyne wkatyy sws vepasps qd tlyavhfq p yadrwqriv dmngalqsea dnfvnatwd d ydtgqina sd vlsanta mse ygvrsg sese glwrs taals mmgy dtpnln nsg mmtveyk nv qhtgllma k napngswqv nttyntsnid gpvfmatte g tkldfadg ee ftivgmt akd gtavns tqtt kyryk tantt elle vqnqli elr qeiedre pe aggffgsg s tdtmlvgll alagvlllaq snnrggrr

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
1.5 MNaClSodium chloride
100.0 mMMgCl2
2.0 mMCaCl2
20.0 mMTris-HClTris
GridModel: Quantifoil R 2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa / Details: Almost at sea level
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 26000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 77.0 K
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4080 pixel / Digitization - Dimensions - Height: 4080 pixel / Digitization - Sampling interval: 15.0 µm / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 17 / Number images used: 3588 / Method: volumes picked interactively / Software - Name: JSUBTOMO
Software - details: Particles were iteratively centered, first against a spherical model of a 17.3-nm radius and then against their own 3D radial density profile, without any symmetry imposed. These ...Software - details: Particles were iteratively centered, first against a spherical model of a 17.3-nm radius and then against their own 3D radial density profile, without any symmetry imposed. These particles were all roughly spherical and were assumed to have the membrane at a similar radius in subsequent steps. This enabled the automatic selection of 3,588 membrane subvolumes from all over the surface of the centered particles, on a regular grid, irrespective of whether or not the volume contained spikes, in a box of 30 by 30 by 30 pixels. A surface normal in each location defined the orientation of each subvolume relative to the viral surface.
Details: 78 initial subtomograms each contained one virus particle were first extractd. These were further dissected to recover 3588 subtomograms containing spikes.
CTF correctionDetails: Data were truncated to the first zero of the CTF
Final angle assignmentType: OTHER / Software - Name: IMOD
Details: The tilt angles are recorded in the microscope software and utilised in the
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Software - Name: IMOD
Details: R-weighted back-projection. The resolution was not estimated quantitatively for this structure, however, I estimate it qualitatively to be around 4 nm.
Number subtomograms used: 1019

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