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- EMDB-14037: Cryo-electron tomogram of EIAV CASPNC VLPs, acquired on Krios 3Gi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-14037 | |||||||||
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Title | Cryo-electron tomogram of EIAV CASPNC VLPs, acquired on Krios 3Gi, Bioquantum K3 | |||||||||
![]() | Example tomogram of EIAV Gag VLPs | |||||||||
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![]() | Retrovirus / Equine infectious anemia virus / capsid protein / VIRAL PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | electron tomography / cryo EM | |||||||||
![]() | Obr M / Hagen WJH / Dick RA / Yu L / Kotecha A / Schur FKM | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Authors: Martin Obr / Wim J H Hagen / Robert A Dick / Lingbo Yu / Abhay Kotecha / Florian K M Schur / ![]() ![]() ![]() ![]() Abstract: The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for ...The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4-6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes. | |||||||||
History |
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Structure visualization
Movie |
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Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 80.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.2 KB 14.2 KB | Display Display | ![]() |
Images | ![]() | 187.3 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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EM raw data | ![]() Data size: 106.2 Data #1: Unaligned movies of EIAV VLPs [micrographs - multiframe] Data #2: Tilt series of EIAV VLPs [tilt series]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Example tomogram of EIAV Gag VLPs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.576 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 : Equine infectious anemia virus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Equine infectious anemia virus
Supramolecule | Name: Equine infectious anemia virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11665 / Sci species name: Equine infectious anemia virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Name: Immature capsid |
-Macromolecule #1: EIAV CASPNC
Macromolecule | Name: EIAV CASPNC / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: SPIMIDGAGN RNFRPLTPRG YTTWVNTIQT NGLLNEASQN LFGILSVDCT SEEMNAFLDV V PGQAGQKQ ILLDAIDKIA DDWDNRHPLP NAPLVAPPQG PIPMTARFIR GLGVPRERQM EP AFDQFRQ TYRQWIIEAM SEGIKVMIGK PKAQNIRQGA KEPYPEFVDR ...String: SPIMIDGAGN RNFRPLTPRG YTTWVNTIQT NGLLNEASQN LFGILSVDCT SEEMNAFLDV V PGQAGQKQ ILLDAIDKIA DDWDNRHPLP NAPLVAPPQG PIPMTARFIR GLGVPRERQM EP AFDQFRQ TYRQWIIEAM SEGIKVMIGK PKAQNIRQGA KEPYPEFVDR LLSQIKSEGH PQE ISKFLT DTLTIQNANE ECRNAMRHLR PEDTLEEKMY ACRDIGTTKQ KMML LAKAL QTGLAGPFK GGALKGGPLK AAQTCYNCGK PGHLSSQCRA PKVCFKCKQP GHFSKQCRSV P KNGKQGAQ GRPQKQTF |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6.2 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP Details: 3.5 seconds blotting time, using back-side blotting. | |||||||||||||||
Sectioning | Other: NO SECTIONING | |||||||||||||||
Fiducial marker | Manufacturer: Aurion / Diameter: 10 nm |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 0.096 sec. / Average electron dose: 3.7 e/Å2 / Details: dose-fractionation: 7 frames / tilted image |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.25 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: eTomo (ver. 4.9.10) Details: Tomogram reconstructed in Etomo using weighted back-projection with SIRT-like lowpass filter. Number images used: 41 |
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