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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8986 | |||||||||
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Title | A 3.1 Angstrom sub-tomogram average of HIV-1 CA-SP1. | |||||||||
![]() | Map with a B-factor of 150 applied, as used in generating figures. | |||||||||
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Method | subtomogram averaging / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Himes BA / Zhang P | |||||||||
![]() | ![]() Title: emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. Authors: Benjamin A Himes / Peijun Zhang / ![]() ![]() Abstract: Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by ...Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by cryo-electron tomography (cryo-ET) combined with subtomogram alignment and classification, which in exceptional cases achieves subnanometer resolution, yielding insight into structure-function relationships. However, it remains challenging to apply this approach to specimens that exhibit conformational or compositional heterogeneity or are present in low abundance. To address this, we developed emClarity ( https://github.com/bHimes/emClarity/wiki ), a GPU-accelerated image-processing package featuring an iterative tomographic tilt-series refinement algorithm that uses subtomograms as fiducial markers and a 3D-sampling-function-compensated, multi-scale principal component analysis classification method. We demonstrate that our approach offers substantial improvement in the resolution of maps and in the separation of different functional states of macromolecular complexes compared with current state-of-the-art software. | |||||||||
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 | ![]() | 15.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.1 KB 10.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 34.9 KB | Display | ![]() |
Images | ![]() | 46.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 79.3 KB | Display | ![]() |
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Full document | ![]() | 78.4 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8799C ![]() 8802C ![]() 8803C ![]() 8804C ![]() 8805C ![]() 8806C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map with a B-factor of 150 applied, as used in generating figures. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 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 : HIV-1 CA-SP1
Entire | Name: HIV-1 CA-SP1 |
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Components |
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-Supramolecule #1: HIV-1 CA-SP1
Supramolecule | Name: HIV-1 CA-SP1 / type: virus / ID: 1 / Parent: 0 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Details | Please refer to EMD-3782/ EMPIAR-10164 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Please refer to EMD-3782/ EMPIAR-10164 |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.4 e/Å2 / Details: Please refer to EMD-3782/ EMPIAR-10164 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |