+Open data
-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 data | Map with a B-factor of 150 applied, as used in generating figures. | |||||||||
Sample |
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Method | subtomogram averaging / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Himes BA / Zhang P | |||||||||
Citation | Journal: Nat Methods / Year: 2018 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8986.map.gz | 15.4 MB | EMDB map data format | |
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Header (meta data) | emd-8986-v30.xml emd-8986.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8986_fsc.xml | 34.9 KB | Display | FSC data file |
Images | emd_8986.png | 46.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8986 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8986 | HTTPS FTP |
-Related structure data
Related structure data | 8799C 8802C 8803C 8804C 8805C 8806C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8986.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map with a B-factor of 150 applied, as used in generating figures. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Details | Please refer to EMD-3782/ EMPIAR-10164 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |