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- EMDB-1907: Electron cryo-microscopy and image reconstruction of adeno-associ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1907
TitleElectron cryo-microscopy and image reconstruction of adeno-associated virus type 2 empty capsids
Map dataAAV-2 empty capsids
Sample
  • Sample: Adeno-associated Virus Type 2
  • Virus: Adeno-associated virus - 2
KeywordsAAV2 / virus / empty capsids
Biological speciesAdeno-associated virus - 2
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsKronenberg S / Kleinschmidt JA / Bottcher B
CitationJournal: EMBO Rep / Year: 2001
Title: Electron cryo-microscopy and image reconstruction of adeno-associated virus type 2 empty capsids.
Authors: S Kronenberg / J A Kleinschmidt / B Böttcher /
Abstract: Adeno-associated virus type 2 empty capsids are composed of three proteins, VP1, VP2 and VP3, which have relative molecular masses of 87, 72 and 62 kDa, respectively, and differ in their N-terminal ...Adeno-associated virus type 2 empty capsids are composed of three proteins, VP1, VP2 and VP3, which have relative molecular masses of 87, 72 and 62 kDa, respectively, and differ in their N-terminal amino acid sequences. They have a likely molar ratio of 1:1:8 and occupy symmetrical equivalent positions in an icosahedrally arranged protein shell. We have investigated empty capsids of adeno-associated virus type 2 by electron cryo-microscopy and icosahedral image reconstruction. The three-dimensional map at 1.05 nm resolution showed sets of three elongated spikes surrounding the three-fold symmetry axes and narrow empty channels at the five-fold axes. The inside of the capsid superimposed with the previously determined structure of the canine parvovirus (Q. Xie and M.S. Chapman, 1996, J. Mol. Biol., 264, 497-520), whereas the outer surface showed clear discrepancies. Globular structures at the inner surface of the capsid at the two-fold symmetry axes were identified as possible positions for the N-terminal extensions of VP1 and VP2.
History
DepositionJun 10, 2011-
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: 12
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1907_aav2_1....

Downloads & links

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Map

FileDownload / File: emd_1907.map.gz / Format: CCP4 / Size: 2.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAAV-2 empty capsids
Voxel sizeX=Y=Z: 4.2 Å
Density
Contour LevelBy AUTHOR: 12.0 / Movie #1: 12
Minimum - Maximum-44.559199999999997 - 61.091700000000003
Average (Standard dev.)-0.0438755 (±9.89312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions838383
Spacing838383
CellA=B=C: 348.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z838383
origin x/y/z-0.000-0.000-0.000
length x/y/z348.600348.600348.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS838383
D min/max/mean-44.55961.092-0.044

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Supplemental data

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Sample components

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Entire : Adeno-associated Virus Type 2

EntireName: Adeno-associated Virus Type 2
Components
  • Sample: Adeno-associated Virus Type 2
  • Virus: Adeno-associated virus - 2

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Supramolecule #1000: Adeno-associated Virus Type 2

SupramoleculeName: Adeno-associated Virus Type 2 / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 3.9 MDa

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Supramolecule #1: Adeno-associated virus - 2

SupramoleculeName: Adeno-associated virus - 2 / type: virus / ID: 1 / Name.synonym: AAV2 / NCBI-ID: 10804 / Sci species name: Adeno-associated virus - 2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Syn species name: AAV2
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 3.9 MDa
Virus shellShell ID: 1 / Name: AAV2 / Diameter: 260 Å / T number (triangulation number): 1

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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: 7.5 / Details: 0.1M NaCl, 1 mM MgCl2, 10 mM Tris-HCl pH 7.5
GridDetails: 400 mesh copper grid, coated with holey carbon, covered with thin continuous carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Controlled environment / Method: blot for 15s before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 6.4 mm / Nominal defocus max: 1.93 µm / Nominal defocus min: 0.81 µm / Nominal magnification: 52000
Sample stageSpecimen holder: Side entry, liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 94 K / Average: 94 K
Alignment procedureLegacy - Astigmatism: At 200,000 magnification on carbon
DateApr 10, 2001
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Number real images: 10 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Combination of defocussed maps
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MRC
Details: Maps were calculated for each micrograph maps were ctf-corrected and averaged ctf-weighted data was corrected for envelope function due to spatial aberration
Number images used: 1800

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