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- EMDB-1907: Electron cryo-microscopy and image reconstruction of adeno-associ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1907 | |||||||||
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Title | Electron cryo-microscopy and image reconstruction of adeno-associated virus type 2 empty capsids | |||||||||
![]() | AAV-2 empty capsids | |||||||||
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![]() | AAV2 / virus / empty capsids | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.5 Å | |||||||||
![]() | Kronenberg S / Kleinschmidt JA / Bottcher B | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.1 KB 9.1 KB | Display Display | ![]() |
Images | ![]() | 26.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 268.5 KB | Display | ![]() |
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Full document | ![]() | 267.7 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AAV-2 empty capsids | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Adeno-associated Virus Type 2
Entire | Name: Adeno-associated Virus Type 2 |
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Components |
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-Supramolecule #1000: Adeno-associated Virus Type 2
Supramolecule | Name: Adeno-associated Virus Type 2 / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 3.9 MDa |
-Supramolecule #1: Adeno-associated virus - 2
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.9 MDa |
Virus shell | Shell ID: 1 / Name: AAV2 / Diameter: 260 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: 0.1M NaCl, 1 mM MgCl2, 10 mM Tris-HCl pH 7.5 |
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Grid | Details: 400 mesh copper grid, coated with holey carbon, covered with thin continuous carbon |
Vitrification | Cryogen 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
Microscope | FEI/PHILIPS CM120T |
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Temperature | Min: 94 K / Average: 94 K |
Alignment procedure | Legacy - Astigmatism: At 200,000 magnification on carbon |
Date | Apr 10, 2001 |
Image recording | Category: 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 min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.4 mm / Nominal defocus max: 1.93 µm / Nominal defocus min: 0.81 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder: Side entry, liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: Combination of defocussed maps |
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Final reconstruction | Applied 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 |