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TitleemClarity: software for high-resolution cryo-electron tomography and subtomogram averaging.
Journal, issue, pagesNat Methods, Vol. 15, Issue 11, Page 955-961, Year 2018
Publish dateOct 22, 2018
AuthorsBenjamin A Himes / Peijun Zhang /
PubMed AbstractMacromolecular 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.
External linksNat Methods / PubMed:30349041 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution3.1 - 11.0 Å
Structure data

EMDB-8799:
Yeast 80S ribosome derived from EMPIAR-10045 using emClarity
Method: EM (subtomogram averaging) / Resolution: 7.8 Å

EMDB-8802:
80S ribsome from Oryctolagus cuniculus, class I - with non-rotated/non-swiveled 40S and P site tRNA, derived from EMPIAR-10064 using eClarity
Method: EM (subtomogram averaging) / Resolution: 9.3 Å

EMDB-8803:
80S ribsome from Oryctolagus cuniculus, class II - with non-rotated/non-swiveled 40S with P site tRNA and ternary complex, derived from EMPIAR-10064 using eClarity
Method: EM (subtomogram averaging) / Resolution: 9.9 Å

EMDB-8804:
80S ribsome from Oryctolagus cuniculus, class III - with non-rotated/non-swiveled 40S with P site and E site tRNA, derived from EMPIAR-10064 using eClarity
Method: EM (subtomogram averaging) / Resolution: 10.2 Å

EMDB-8805:
80S ribsome from Oryctolagus cuniculus, class IV - with mid-rotated/swiveled 40S and eeF2, derived from EMPIAR-10064 using eClarity
Method: EM (subtomogram averaging) / Resolution: 9.8 Å

EMDB-8806:
80S ribsome from Oryctolagus cuniculus, class V - with mid-rotated/swiveled 40S and eeF2, derived from EMPIAR-10064 using eClarity
Method: EM (subtomogram averaging) / Resolution: 11.0 Å

EMDB-8986:
A 3.1 Angstrom sub-tomogram average of HIV-1 CA-SP1.
Method: EM (subtomogram averaging) / Resolution: 3.1 Å

Source
  • Saccharomyces cerevisiae (brewer's yeast)
  • Oryctolagus cuniculus (rabbit)

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