5M3L

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin

Summary for 5M3L

• Entry DOI: 10.2210/pdb5m3l/pdb
• EMDB information: 3434
• Descriptor: Extracellular globin-4, Extracellular globin-2, Extracellular globin-3, ... (8 entities in total)
• Functional Keywords: lumbricus terrestris, hemoglobin, oxygen carrier, erythrocruorin, oxygen transport
• Biological source: Lumbricus terrestris (Common earthworm); More
• Total number of polymer chains: 15
• Total formula weight: 283371.46

Authors

Afanasyev, P.,Linnemayr-Seer, C.,Ravelli, R.B.G.,Matadeen, R.,De Carlo, S.,Alewijnse, B.,Portugal, R.V.,Pannu, N.S.,Schatz, M.,van Heel, M. (deposition date: 2016-10-15, release date: 2017-09-13, Last modification date: 2024-05-08)

Primary citation

Afanasyev, P.,Seer-Linnemayr, C.,Ravelli, R.B.G.,Matadeen, R.,De Carlo, S.,Alewijnse, B.,Portugal, R.V.,Pannu, N.S.,Schatz, M.,van Heel, M.
Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.
IUCrJ, 4:678-694, 2017

PubMed Abstract: 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.

PubMed: 28989723
DOI: 10.1107/S2052252517010922

Experimental method

ELECTRON MICROSCOPY (3.8 Å)