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TitleSingle-particle cryo-EM using alignment by classification (ABC): the structure of haemoglobin.
Journal, issue, pagesIUCrJ, Vol. 4, Issue Pt 5, Page 678-694, Year 2017
Publish dateSep 1, 2017
AuthorsPavel Afanasyev / Charlotte Seer-Linnemayr / Raimond B G Ravelli / Rishi Matadeen / Sacha De Carlo / Bart Alewijnse / Rodrigo V Portugal / Navraj S Pannu / Michael Schatz / Marin van Heel /
PubMed AbstractSingle-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in ...Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.
External linksIUCrJ / PubMed:28989723 / PubMed Central
MethodsEM (single particle)
Resolution3.8 Å
Structure data

3434

5m3l

EMDB-3434: Single-particle cryo-EM using alignment by classification (ABC):Lumbricus terrestris hemoglobin at near-atomic resolution
PDB-5m3l: Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

Source
  • lumbricus terrestris (common earthworm)
KeywordsOXYGEN TRANSPORT / Lumbricus terrestris / hemoglobin / oxygen carrier / erythrocruorin

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