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- EMDB-1489: Human Adenovirus type 5 with 31 residue extension at the N-termin... -

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Basic information

Entry
Database: EMDB / ID: EMD-1489
TitleHuman Adenovirus type 5 with 31 residue extension at the N-terminus of polypeptide IIIa
Map dataHuman adenovirus type 5
Sample
  • Sample: Human adenovirus type 5
  • Virus: Human adenovirus 5
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsSan Martin C / Glasgow JN / Borovjagin A / Beatty MS / Kashentseva EA / Curiel DT / Marabini R / Dmitriev IP
CitationJournal: J Mol Biol / Year: 2008
Title: Localization of the N-terminus of minor coat protein IIIa in the adenovirus capsid.
Authors: Carmen San Martín / Joel N Glasgow / Anton Borovjagin / Matthew S Beatty / Elena A Kashentseva / David T Curiel / Roberto Marabini / Igor P Dmitriev /
Abstract: Minor coat protein IIIa is conserved in all adenoviruses (Ads) and is required for correct viral assembly, but its precise function in capsid organization is unknown. The latest Ad capsid model ...Minor coat protein IIIa is conserved in all adenoviruses (Ads) and is required for correct viral assembly, but its precise function in capsid organization is unknown. The latest Ad capsid model proposes that IIIa is located underneath the vertex region. To obtain experimental evidence on the location of IIIa and to further define its role, we engineered the IIIa gene to encode heterologous N-terminal peptide extensions. Recombinant Ad variants with IIIa encoding six-histidine (6His) tag, 6His, and FLAG peptides, or with 6His linked to FLAG with a (Gly(4)Ser)(3) linker were rescued and analyzed for virus yield, capsid incorporation of heterologous peptides, and capsid stability. Longer extensions could not be rescued. Western blot analysis confirmed that the modified IIIa proteins were expressed in infected cells and incorporated into virions. In the Ad encoding the 6His-linker-FLAG-IIIa gene, the 6His tag was present in light particles, but not in mature virions. Immunoelectron microscopy of this virus showed that the FLAG epitope is not accessible to antibodies on the viral particles. Three-dimensional electron microscopy and difference mapping located the IIIa N-terminal extension beneath the vertex complex, wedged at the interface between the penton base and peripentonal hexons, therefore supporting the latest proposed model. The position of the IIIa N-terminus and its low tolerance for modification provide new clues for understanding the role of this minor coat protein in Ad capsid assembly and disassembly.
History
DepositionMar 3, 2008-
Header (metadata) releaseMar 5, 2008-
Map releaseApr 9, 2009-
UpdateApr 20, 2009-
Current statusApr 20, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1489.gif

Downloads & links

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Map

FileDownload / File: emd_1489.map.gz / Format: CCP4 / Size: 77.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman adenovirus type 5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 275 pix.
= 1155. Å		4.2 Å/pix.
x 275 pix.
= 1155. Å		4.2 Å/pix.
x 275 pix.
= 1155. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.788 / Movie #1: 0.55
Minimum - Maximum-2.10264 - 3.37466
Average (Standard dev.)-0.257462 (±0.591087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions275275275
Spacing275275275
CellA=B=C: 1155 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z275275275
origin x/y/z0.0000.0000.000
length x/y/z1155.0001155.0001155.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS275275275
D min/max/mean-2.1033.375-0.257

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Supplemental data

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Sample components

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Entire : Human adenovirus type 5

EntireName: Human adenovirus type 5
Components
  • Sample: Human adenovirus type 5
  • Virus: Human adenovirus 5

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Supramolecule #1000: Human adenovirus type 5

SupramoleculeName: Human adenovirus type 5 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / Name.synonym: Ad5 / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: Ad5
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 150 MDa / Theoretical: 150 MDa
Virus shellShell ID: 1 / Diameter: 900 Å

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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: 7.2 / Details: 10 mM phosphate pH 7.2, 150 mM NaCl
GridDetails: Quantifoil R2/4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC / Details: Vitrification instrument: Leica CPC

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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: 2.2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.7 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 / Number real images: 89 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flip in micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider,xmipp / Number images used: 3171

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