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- EMDB-1839: Conformational changes of Adeno-associated Virus type 1 induced b... -

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Basic information

Entry
Database: EMDB / ID: EMD-1839
TitleConformational changes of Adeno-associated Virus type 1 induced by genome packaging
Map dataMap of Adeno-associated Virus Type 1, group 4 (full capsids).
Sample
  • Sample: Adeno-associated Virus Type 1
  • Virus: Adeno-associated virus - 1
KeywordsAAV-1 / virus / structure
Biological speciesAdeno-associated virus - 1
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 9.6 Å
AuthorsGerlach B / Kleinschmidt JA / Bottcher B
CitationJournal: J Mol Biol / Year: 2011
Title: Conformational changes in adeno-associated virus type 1 induced by genome packaging.
Authors: Britta Gerlach / Jürgen A Kleinschmidt / Bettina Böttcher /
Abstract: Adeno-associated virus (AAV) is frequently used as a vector for gene therapy. The viral capsid consists of three structural proteins (VP1, VP2, and VP3) that have a common C-terminal core (VP3), with ...Adeno-associated virus (AAV) is frequently used as a vector for gene therapy. The viral capsid consists of three structural proteins (VP1, VP2, and VP3) that have a common C-terminal core (VP3), with N-terminal extensions of increasing length in VP2 and VP1. The capsid encloses a single-stranded genome of up to 4.7 kb, which is packaged into empty capsids. The N-terminal extension of VP1 carries a phospholipase domain that becomes accessible during infection in the endosomal pathway. We have used cryo-electron microscopy and image reconstruction to determine subnanometer-resolution structures of recombinant AAV1 that has packaged different amounts of a 3.6-kb recombinant genome. The maps show that the AAV1 capsid undergoes continuous conformational changes upon packaging of the genome. The rearrangements occur at the inner capsid surface and lead to constrictions of the pores at the 5-fold symmetry axes and to subtle movements of the β-sheet regions of the capsid proteins. In fully packaged particles, the genome forms stem-like features that contact the inner capsid surface at the 3-fold symmetry axes. We think that the reorganization of the inner surface has an impact on the viral life cycle during infection, preparing the externalization of phospholipase domains through the pores at the 5-fold symmetry axes and possibly genome release.
History
DepositionNov 29, 2010-
Header (metadata) releaseJun 30, 2011-
Map releaseJun 30, 2011-
UpdateJun 30, 2011-
Current statusJun 30, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1839.map.gz / Format: CCP4 / Size: 6.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of Adeno-associated Virus Type 1, group 4 (full capsids).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 123 pix.
= 344.4 Å
2.8 Å/pix.
x 123 pix.
= 344.4 Å
2.8 Å/pix.
x 123 pix.
= 344.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour LevelBy AUTHOR: 4.6 / Movie #1: 4.6
Minimum - Maximum-14.0382 - 27.782299999999999
Average (Standard dev.)-0.0123085 (±4.33888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions123123123
Spacing123123123
CellA=B=C: 344.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z123123123
origin x/y/z0.0000.0000.000
length x/y/z344.400344.400344.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS123123123
D min/max/mean-14.03827.782-0.012

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Supplemental data

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Sample components

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Entire : Adeno-associated Virus Type 1

EntireName: Adeno-associated Virus Type 1
Components
  • Sample: Adeno-associated Virus Type 1
  • Virus: Adeno-associated virus - 1

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Supramolecule #1000: Adeno-associated Virus Type 1

SupramoleculeName: Adeno-associated Virus Type 1 / type: sample / ID: 1000
Details: Recombinant AAV1 capsid, particles belong to group 4 (full capsids).
Oligomeric state: VP1, VP2, and VP3 in T1 arrangement / Number unique components: 1

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Supramolecule #1: Adeno-associated virus - 1

SupramoleculeName: Adeno-associated virus - 1 / type: virus / ID: 1 / Name.synonym: AAV 1 / NCBI-ID: 85106 / Sci species name: Adeno-associated virus - 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Syn species name: AAV 1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 240 Å / T number (triangulation number): 1

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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

StainingType: NEGATIVE / Details: Vitrified
GridDetails: 400 mesh perforated carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 96 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Controlled environment / Method: Blot for 15 s before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: Astigmatism was corrected at 200,000 times magnification on graininess of carbon
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 105 / Details: Data binning 2x2 pixels, before processing. / Bits/pixel: 8

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Image processing

CTF correctionDetails: Maps during combination
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MRC / Number images used: 3197
DetailsParticles were sorted according to their density profiles. This reconstructions represents group 4, which consists of filled capsids.

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