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- EMDB-1586: Human Adenovirus type 2 ts1 mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-1586
TitleHuman Adenovirus type 2 ts1 mutant
Map dataHuman adenovirus type 5 at 8.9 Angstrom resolution, showing the structure of the mature, infective virion
Sample
  • Sample: Human adenovirus type 2, ts1 mutant produced at 39 degrees
  • Virus: Human adenovirus 2
Biological speciesHuman adenovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsPerez-Berna AJ / Marabini R / Scheres SHW / Menendez-Conejero R / Dmitriev IP / Curiel DT / Mangel WF / Flint SJ / San Martin C
CitationJournal: J Mol Biol / Year: 2009
Title: Structure and uncoating of immature adenovirus.
Authors: Ana J Pérez-Berná / Roberto Marabini / Sjors H W Scheres / Rosa Menéndez-Conejero / Igor P Dmitriev / David T Curiel / Walter F Mangel / S Jane Flint / Carmen San Martín /
Abstract: Maturation via proteolytic processing is a common trait in the viral world and is often accompanied by large conformational changes and rearrangements in the capsid. The adenovirus protease has been ...Maturation via proteolytic processing is a common trait in the viral world and is often accompanied by large conformational changes and rearrangements in the capsid. The adenovirus protease has been shown to play a dual role in the viral infectious cycle: (a) in maturation, as viral assembly starts with precursors to several of the structural proteins but ends with proteolytically processed versions in the mature virion, and (b) in entry, because protease-impaired viruses have difficulties in endosome escape and uncoating. Indeed, viruses that have not undergone proteolytic processing are not infectious. We studied the three-dimensional structure of immature adenovirus particles as represented by the adenovirus type 2 thermosensitive mutant ts1 grown under non-permissive conditions and compared it with the mature capsid. Our three-dimensional electron microscopy maps at subnanometer resolution indicate that adenovirus maturation does not involve large-scale conformational changes in the capsid. Difference maps reveal the locations of unprocessed peptides pIIIa and pVI and help define their role in capsid assembly and maturation. An intriguing difference appears in the core, indicating a more compact organization and increased stability of the immature cores. We have further investigated these properties by in vitro disassembly assays. Fluorescence and electron microscopy experiments reveal differences in the stability and uncoating of immature viruses, both at the capsid and core levels, as well as disassembly intermediates not previously imaged.
History
DepositionApr 8, 2009-
Header (metadata) releaseApr 15, 2009-
Map releaseJul 2, 2009-
UpdateDec 25, 2013-
Current statusDec 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1586.png

Downloads & links

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Map

FileDownload / File: emd_1586.map.gz / Format: CCP4 / Size: 253 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman adenovirus type 5 at 8.9 Angstrom resolution, showing the structure of the mature, infective virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 408 pix.
= 1126.08 Å		2.76 Å/pix.
x 408 pix.
= 1126.08 Å		2.76 Å/pix.
x 408 pix.
= 1126.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.25 / Movie #1: 0.5
Minimum - Maximum-2.96093 - 4.52003
Average (Standard dev.)-0.138364 (±0.545806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 1126.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z408408408
origin x/y/z0.0000.0000.000
length x/y/z1126.0801126.0801126.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS408408408
D min/max/mean-2.9614.520-0.138

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Supplemental data

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Sample components

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Entire : Human adenovirus type 2, ts1 mutant produced at 39 degrees

EntireName: Human adenovirus type 2, ts1 mutant produced at 39 degrees
Components
  • Sample: Human adenovirus type 2, ts1 mutant produced at 39 degrees
  • Virus: Human adenovirus 2

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Supramolecule #1000: Human adenovirus type 2, ts1 mutant produced at 39 degrees

SupramoleculeName: Human adenovirus type 2, ts1 mutant produced at 39 degrees
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human adenovirus 2

SupramoleculeName: Human adenovirus 2 / type: virus / ID: 1 / Name.synonym: Adenovirus / NCBI-ID: 10515 / Sci species name: Human adenovirus 2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: Adenovirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 950 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: 7.4
Details: PBS (8 mM Na2HPO4, 2 mM KH2PO4, 137 mM NaCl, 2.7 mM KCl)
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: 2.26 mm / Nominal defocus max: 5.1 µm / Nominal defocus min: 0.5 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: 297 / 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: 8.7 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: xmipp, ctffind / Number images used: 9188

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Atomic model buiding 1

Initial modelPDB ID:

1bld


Chain - Chain ID: A
SoftwareName: URO
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT

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