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- EMDB-1272: Cryoelectron microscopy of protein IX-modified adenoviruses sugge... -

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Basic information

Entry
Database: EMDB / ID: EMD-1272
TitleCryoelectron microscopy of protein IX-modified adenoviruses suggests a new position for the C terminus of protein IX.
Map dataThis is the reconstruction of Ad-IX-GFP capsids. The data were collected at 2.17 angstrom per pixel and downsampled by 2 for processing. The final reconstruction was guassian lowpass filtered to 22 angstroms. The map deposited here is oriented with the 3-fold axis along z. This map is a half-map.
Sample
  • Sample: Adenovirus capsid with GFP fused to C-terminus of capisd protein pIX
  • Virus: Human adenovirus 5
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsMarsh MP / Campos SK / Baker ML / Chen CY / Chiu W / Barry MA
CitationJournal: J Virol / Year: 2006
Title: Cryoelectron microscopy of protein IX-modified adenoviruses suggests a new position for the C terminus of protein IX.
Authors: Michael P Marsh / Samuel K Campos / Matthew L Baker / Christopher Y Chen / Wah Chiu / Michael A Barry /
Abstract: Recombinant human adenovirus is a useful gene delivery vector for clinical gene therapy. Minor capsid protein IX of adenovirus has been of recent interest since multiple studies have shown that ...Recombinant human adenovirus is a useful gene delivery vector for clinical gene therapy. Minor capsid protein IX of adenovirus has been of recent interest since multiple studies have shown that modifications can be made to its C terminus to alter viral tropism or add molecular tags and/or reporter proteins. We examined the structure of an engineered adenovirus displaying the enhanced green fluorescent protein (EGFP) fused to the C terminus of protein IX. Cryoelectron microscopy and reconstruction localized the C-terminal EGFP fusion between the H2 hexon and the H4 hexon, positioned between adjacent facets, directly above the density previously assigned as protein IIIa. The original assignment of IIIa was based largely on indirect evidence, and the data presented herein support the reassignment of the IIIa density as protein IX.
History
DepositionOct 4, 2006-
Header (metadata) releaseOct 4, 2006-
Map releaseOct 4, 2006-
UpdateOct 31, 2012-
Current statusOct 31, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.298488502
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.298488502
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1272.gif

Downloads & links

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Map

FileDownload / File: emd_1272.map.gz / Format: CCP4 / Size: 60.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the reconstruction of Ad-IX-GFP capsids. The data were collected at 2.17 angstrom per pixel and downsampled by 2 for processing. The final reconstruction was guassian lowpass filtered to 22 angstroms. The map deposited here is oriented with the 3-fold axis along z. This map is a half-map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.34 Å/pix.
x 160 pix.
= 690.06 Å		4.34 Å/pix.
x 319 pix.
= 1380.12 Å		4.34 Å/pix.
x 319 pix.
= 1380.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.34 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.25 / Movie #1: 2.2984885
Minimum - Maximum-4.145 - 5.91242
Average (Standard dev.)0.0000000030212 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-159-159-80
Dimensions319319160
Spacing319319160
CellA: 1380.12 Å / B: 1380.12 Å / C: 690.06 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.344.344.34
M x/y/z318318159
origin x/y/z0.0000.0000.000
length x/y/z1380.1201380.120690.060
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-159-159-80
NC/NR/NS319319160
D min/max/mean-4.1455.9120.000

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Supplemental data

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Sample components

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Entire : Adenovirus capsid with GFP fused to C-terminus of capisd protein pIX

EntireName: Adenovirus capsid with GFP fused to C-terminus of capisd protein pIX
Components
  • Sample: Adenovirus capsid with GFP fused to C-terminus of capisd protein pIX
  • Virus: Human adenovirus 5

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Supramolecule #1000: Adenovirus capsid with GFP fused to C-terminus of capisd protein pIX

SupramoleculeName: Adenovirus capsid with GFP fused to C-terminus of capisd protein pIX
type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 150 MDa

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Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / Name.synonym: Adenovirus, Ad-IX-GFP / Details: GFP fusion to protein pIX / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: Adenovirus, Ad-IX-GFP
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 150 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 920 Å / T number (triangulation number): 25

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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: Phosphate-buffered Saline (PBS)
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blotted twice for one second each.

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Electron microscopy

MicroscopeJEOL 2010F
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: 18.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.This holder operates in the temperature range from 77K to ambient.
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 77 K
DateDec 17, 2004
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 2.17 µm / Number real images: 100 / Average electron dose: 15 e/Å2 / Bits/pixel: 16

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SAVR / Number images used: 800

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