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- EMDB-1739: Human Bocavirus Capsid structure: Insights into the structural re... -

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Entry
Database: EMDB / ID: EMD-1739
TitleHuman Bocavirus Capsid structure: Insights into the structural repertoire of the Parvoviridae
Map dataThis is a cryo-reconstruction of human bocavirus (HBoV) from virus-like particles of viral protein 2 (VP2)
Sample
  • Sample: Virus-like particles of human Bocavirus viral protein 2
  • Virus: Human bocavirus
KeywordsHuman Bocavirus / Parvovirus / Virus structure / Electron Cryo-Microscopy / 3D Image Reconstruction / Structural Evolution
Biological speciesHuman bocavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsGurda BL / Parent KN / Bladek H / Sinkovits RS / DiMattia MA / Rence C / Castro A / McKenna R / Olson N / Brown K ...Gurda BL / Parent KN / Bladek H / Sinkovits RS / DiMattia MA / Rence C / Castro A / McKenna R / Olson N / Brown K / Baker TS / Agbandje-McKenna M
CitationJournal: J Virol / Year: 2010
Title: Human bocavirus capsid structure: insights into the structural repertoire of the parvoviridae.
Authors: Brittney L Gurda / Kristin N Parent / Heather Bladek / Robert S Sinkovits / Michael A DiMattia / Chelsea Rence / Alejandro Castro / Robert McKenna / Norm Olson / Kevin Brown / Timothy S ...Authors: Brittney L Gurda / Kristin N Parent / Heather Bladek / Robert S Sinkovits / Michael A DiMattia / Chelsea Rence / Alejandro Castro / Robert McKenna / Norm Olson / Kevin Brown / Timothy S Baker / Mavis Agbandje-McKenna /
Abstract: Human bocavirus (HBoV) was recently discovered and classified in the Bocavirus genus (family Parvoviridae, subfamily Parvovirinae) on the basis of genomic similarity to bovine parvovirus and canine ...Human bocavirus (HBoV) was recently discovered and classified in the Bocavirus genus (family Parvoviridae, subfamily Parvovirinae) on the basis of genomic similarity to bovine parvovirus and canine minute virus. HBoV has been implicated in respiratory tract infections and gastroenteric disease in children worldwide, yet despite numerous epidemiological reports, there has been limited biochemical and molecular characterization of the virus. Reported here is the three-dimensional structure of recombinant HBoV capsids, assembled from viral protein 2 (VP2), at 7.9-A resolution as determined by cryo-electron microscopy and image reconstruction. A pseudo-atomic model of HBoV VP2 was derived from sequence alignment analysis and knowledge of the crystal structure of human parvovirus B19 (genus Erythrovirus). Comparison of the HBoV capsid structure to that of parvoviruses from five separate genera demonstrates strong conservation of a beta-barrel core domain and an alpha-helix, from which emanate several loops of various lengths and conformations, yielding a unique surface topology that differs from the three already described for this family. The highly conserved core is consistent with observations for other single-stranded DNA viruses, and variable surface loops have been shown to confer the host-specific tropism and the diverse antigenic properties of this family.
History
DepositionJun 1, 2010-
Header (metadata) releaseJun 11, 2010-
Map releaseJun 11, 2010-
UpdateJun 11, 2010-
Current statusJun 11, 2010Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 150
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 150
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1739.map.gz / Format: CCP4 / Size: 12.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThis is a cryo-reconstruction of human bocavirus (HBoV) from virus-like particles of viral protein 2 (VP2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 187 pix.
= 335.665 Å
1.8 Å/pix.
x 187 pix.
= 335.665 Å
1.8 Å/pix.
x 187 pix.
= 335.665 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.795 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 150
Minimum - Maximum-513.0 - 1117.0
Average (Standard dev.)37.069499999999998 (±199.756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions187187187
Spacing187187187
CellA=B=C: 335.665 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.7951.7951.795
M x/y/z187187187
origin x/y/z0.0000.0000.000
length x/y/z335.665335.665335.665
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS187187187
D min/max/mean-513.0001117.00037.070

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Supplemental data

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Sample components

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Entire : Virus-like particles of human Bocavirus viral protein 2

EntireName: Virus-like particles of human Bocavirus viral protein 2
Components
  • Sample: Virus-like particles of human Bocavirus viral protein 2
  • Virus: Human bocavirus

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Supramolecule #1000: Virus-like particles of human Bocavirus viral protein 2

SupramoleculeName: Virus-like particles of human Bocavirus viral protein 2
type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1
Molecular weightTheoretical: 3.66 MDa

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Supramolecule #1: Human bocavirus

SupramoleculeName: Human bocavirus / type: virus / ID: 1 / Name.synonym: HBoV / NCBI-ID: 329641 / Sci species name: Human bocavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: HBoV
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 3.66 MDa
Virus shellShell ID: 1 / Name: Viral protein 2 / Diameter: 280 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

Concentration10 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl, 150 mM NaCl, 2 mM MgCl2
GridDetails: Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual plunge-freezer / Method: Blot for 5 sec before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 3.25 µm / Nominal defocus min: 0.95 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Polara Multi Specimen Holder / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: Corrected at 39,000 x magnification with FFT
DateApr 22, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 1.795 µm / Number real images: 16 / Average electron dose: 9 e/Å2 / Od range: 1.5 / Bits/pixel: 8
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: ROBEM
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 3754

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