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- EMDB-1575: C-terminal domain of adenovirus serotype 5 protein IX assemble in... -

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Basic information

Entry
Database: EMDB / ID: EMD-1575
TitleC-terminal domain of adenovirus serotype 5 protein IX assemble into an anti-parallel structure
Map dataAdenovirus sy12 with anti-sy12 fab
Sample
  • Sample: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab
  • Virus: Human adenovirus 5
Keywordsadenovirus / proteinIX / Fab
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 22.0 Å
AuthorsFabry CMS / Rosa-Calatrava M / Moriscot C / Ruigrok RWH / Boulanger P / Schoehn G
CitationJournal: J Virol / Year: 2009
Title: The C-terminal domains of adenovirus serotype 5 protein IX assemble into an antiparallel structure on the facets of the capsid.
Authors: Céline M S Fabry / Manuel Rosa-Calatrava / Christine Moriscot / Rob W H Ruigrok / Pierre Boulanger / Guy Schoehn /
Abstract: Adenovirus serotype 5 protein IX (pIX) has two domains connected by a flexible linker. Three N-terminal domains form triskelions on the capsid facets that cement hexons together, and the C-terminal ...Adenovirus serotype 5 protein IX (pIX) has two domains connected by a flexible linker. Three N-terminal domains form triskelions on the capsid facets that cement hexons together, and the C-terminal domains of four monomers form complexes toward the facet periphery. Here we present a cryoelectron microscopy structure of recombinant adenovirus with a peptide tag added to the C terminus of pIX. The structure, made up by several C termini of pIX, is longer at both ends than the wild-type protein, and Fabs directed against the tag bind to both ends of the oligomer, demonstrating that the pIX C termini associate in an antiparallel manner.
History
DepositionOct 23, 2008-
Header (metadata) releaseOct 23, 2008-
Map releaseNov 12, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -90
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: -90
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1575.png

Downloads & links

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Map

FileDownload / File: emd_1575.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationAdenovirus sy12 with anti-sy12 fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 447 pix.
= 1135.38 Å		2.54 Å/pix.
x 447 pix.
= 1135.38 Å		2.54 Å/pix.
x 447 pix.
= 1135.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 80.0 / Movie #1: -90
Minimum - Maximum-758.0 - 702.0
Average (Standard dev.)-2.12962 (±91.939800000000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-202-202-2
Dimensions447447447
Spacing447447447
CellA=B=C: 1135.38 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.542.542.54
M x/y/z447447447
origin x/y/z0.0000.0000.000
length x/y/z1135.3801135.3801135.380
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-202-202-2
NC/NR/NS447447447
D min/max/mean-758.000702.000-2.130

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Supplemental data

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Sample components

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Entire : SY12 modified adenovirus 5 plus rabbit anti SY12 Fab

EntireName: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab
Components
  • Sample: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab
  • Virus: Human adenovirus 5

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Supramolecule #1000: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab

SupramoleculeName: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab / type: sample / ID: 1000
Details: dodecapeptide TAYSSYMKGGKF (abbreviated SY12 ) fused to the C-terminus of pIX and a recombinant Ad5LacZ-pIX-SY12 vector has been constructed anti SY12 IgG have been clived into FAb using ...Details: dodecapeptide TAYSSYMKGGKF (abbreviated SY12 ) fused to the C-terminus of pIX and a recombinant Ad5LacZ-pIX-SY12 vector has been constructed anti SY12 IgG have been clived into FAb using papain and then purified. The complex have been generated using an excess of Fab
Number unique components: 1

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Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / Name.synonym: adenovirus 5
Details: anti SY12 Fab attached to the C-terminal part of adenovirus 5 protein IX
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 5
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 150 MDa
Virus shellShell ID: 1 / Diameter: 1000 Å / T number (triangulation number): 25

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1. mg/mL
BufferpH: 7.5 / Details: 20mM NaCl, 10mM Tris-HCL
StainingType: NEGATIVE / Details: Cryo EM
GridDetails: Quantifoil r2/2
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Zeiss / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.4 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 11 / Average electron dose: 9 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: pft2 em3dr2 / Number images used: 949
DetailsFab-adenovirus complex

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