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- EMDB-5467: 4.2 Angstrom Cryo-EM structure of Ad5F35 -

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Basic information

Entry
Database: EMDB / ID: EMD-5467
Title4.2 Angstrom Cryo-EM structure of Ad5F35
Map data4.2 Angstrom Cryo-EM reconstruction of Ad5F35
Sample
  • Sample: Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an Ad35 fiber
  • Virus: Human adenovirus 5
Keywordshuman adenovirus / fiber / cryo-EM / near-atomic resolution
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsCao C / Dong X / Wu X / Ji G / Cheng L / Liu H
CitationJournal: J Virol / Year: 2012
Title: Conserved fiber-penton base interaction revealed by nearly atomic resolution cryo-electron microscopy of the structure of adenovirus provides insight into receptor interaction.
Authors: Changchun Cao / Xiaoyan Dong / Xiaobing Wu / Boyun Wen / Gang Ji / Lingpeng Cheng / Hongrong Liu /
Abstract: Adenovirus (Ad) cell attachment is initiated by the attachment of the fiber protein to a primary receptor (usually CAR or CD46). This event is followed by the engagement of the penton base protein ...Adenovirus (Ad) cell attachment is initiated by the attachment of the fiber protein to a primary receptor (usually CAR or CD46). This event is followed by the engagement of the penton base protein with a secondary receptor (integrin) via its loop region, which contains an Arg-Gly-Asp (RGD) motif, to trigger virus internalization. To understand the well-orchestrated adenovirus cell attachment process that involves the fiber and the penton base, we reconstructed the structure of an Ad5F35 capsid, comprising an adenovirus type 5 (Ad5) capsid pseudotyped with an Ad35 fiber, at a resolution of approximately 4.2 Å. The fiber-penton base interaction in the cryo-electron microscopic (cryo-EM) structure of Ad5F35 is similar to that in the cryo-EM structure of Ad5, indicating that the fiber-penton base interaction of adenovirus is conserved. Our structure also confirms that the C-terminal segment of the fiber tail domain constitutes the bottom trunk of the fiber shaft. Based on the conserved fiber-penton base interaction, we have proposed a model for the interaction of Ad5F35 with its primary and secondary receptors. This model could provide insight for designing adenovirus gene delivery vectors.
History
DepositionAug 10, 2012-
Header (metadata) releaseJul 3, 2013-
Map releaseOct 16, 2013-
UpdateOct 16, 2013-
Current statusOct 16, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5467_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5467.map.gz / Format: CCP4 / Size: 897.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation4.2 Angstrom Cryo-EM reconstruction of Ad5F35
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 13.0 / Movie #1: 13
Minimum - Maximum-66.919540409999996 - 89.600265500000006
Average (Standard dev.)1.78658485 (±7.64361334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-392-3920
Dimensions784784392
Spacing784784392
CellA: 901.6 Å / B: 901.6 Å / C: 450.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z784784392
origin x/y/z0.0000.0000.000
length x/y/z901.600901.600450.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-392-3920
NC/NR/NS784784392
D min/max/mean-66.92089.6001.787

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Supplemental data

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Segmentation: Ad5F35 monomer averaged from the 12 hexon monomers...

AnnotationAd5F35 monomer averaged from the 12 hexon monomers in an asymmetric unit of the icosahedron
Fileemd_5467_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an...

EntireName: Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an Ad35 fiber
Components
  • Sample: Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an Ad35 fiber
  • Virus: Human adenovirus 5

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Supramolecule #1000: Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an...

SupramoleculeName: Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an Ad35 fiber
type: sample / ID: 1000 / Number unique components: 7

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Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 930 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

VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateOct 9, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 4500 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMIRS, recISAFs / Number images used: 2100
DetailsViruses in the grid with thin ice were imaged with an FEI 300-kV Titan Krios cryoelectron microscope equipped with a Gatan UltraScan4000 (model 895) 16-megapixel CCD.

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Atomic model buiding 1

Initial modelPDB ID:

3iyn
PDB Unreleased entry

SoftwareName: Chimera
RefinementSpace: REAL

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