5M3L

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history


Literature

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

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.

(2017) IUCrJ 4: 678-694

  • DOI: 10.1107/S2052252517010922
  • Primary Citation of Related Structures:  
    5M3L

  • 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) ...

    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 a posteriori 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 versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.


    Organizational Affiliation

    Department of Life Sciences, Imperial College London, England.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin-4A, E, I151Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P13579 (Lumbricus terrestris)
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Go to UniProtKB:  P13579
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UniProt GroupP13579
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin-2B, F, J145Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P02218 (Lumbricus terrestris)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular globin-3C, G, K153Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P11069 (Lumbricus terrestris)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin chain d1D, H, L140Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for O61233 (Lumbricus terrestris)
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UniProt GroupO61233
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin linker chain L1M217Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q9GV76 (Lumbricus terrestris)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L2 subunitN220Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I743 (Lumbricus terrestris)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L3 subunitO215Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I742 (Lumbricus terrestris)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Dutch ministry of economic affairsNetherlandsCyttron II FES-0908;
NanoNextNL of the Government of the Netherlands and 130 partnersNetherlandsHTS&M Initiative: FES-0901;
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/G015236/1
The Netherlands Organization for Scientific ResearchNetherlandsNWO grant: 016.072.321
Brazilian science foundationBrazilCNPq-152746/2012-9
Brazilian science foundationBrazilCNPq-400796/2012-0

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Other, Refinement description
  • Version 1.3: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2019-12-11
    Changes: Other