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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11008 | |||||||||
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Title | Icosahedral reconstruction of human adenovirus D26 capsid | |||||||||
![]() | Icosahedral map of human adenovirus D26 capsid | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Huiskonen JT / Abrishami V | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. Authors: Vahid Abrishami / Serban L Ilca / Josue Gomez-Blanco / Ilona Rissanen / José Miguel de la Rosa-Trevín / Vijay S Reddy / José-Maria Carazo / Juha T Huiskonen / ![]() ![]() ![]() ![]() ![]() ![]() Abstract: Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM ...Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes. | |||||||||
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 | ![]() | 5.9 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.1 KB 19.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 42.2 KB | Display | ![]() |
Images | ![]() | 211.4 KB | ||
Masks | ![]() | 6.4 GB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 999.2 MB 999.2 MB 5.3 GB 5.3 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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EM raw data | ![]() Data size: 46.5 Data #1: Particle stacks of human adenovirus HAdV-D26 [picked particles - single frame - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Icosahedral map of human adenovirus D26 capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_11008_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_11008_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half 1 of human adenovirus D26 capsid map
File | emd_11008_half_map_1.map | ||||||||||||
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Annotation | Half 1 of human adenovirus D26 capsid map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half 2 of human adenovirus D26 capsid map
File | emd_11008_half_map_2.map | ||||||||||||
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Annotation | Half 2 of human adenovirus D26 capsid map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Icosahedral reconstruction of human adenovirus D26
Entire | Name: Icosahedral reconstruction of human adenovirus D26 |
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Components |
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-Supramolecule #1: Icosahedral reconstruction of human adenovirus D26
Supramolecule | Name: Icosahedral reconstruction of human adenovirus D26 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #2: A composite volume of human adenovirus D26 capsid created from lo...
Supramolecule | Name: A composite volume of human adenovirus D26 capsid created from localized reconstructions of the four hexons type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | ||||||||||||
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Buffer | pH: 8.1 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 7-38 / Number real images: 2000 / Average exposure time: 7.6 sec. / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |