hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding 類似検索 - 分子機能
Lipocalin - #620 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1520 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1530 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1540 / Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin ...Lipocalin - #620 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1520 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1530 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1540 / Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin / Low-density lipoprotein receptor domain class A / Myoglobin-like, M family globin domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Lipocalin / Helix non-globular / Globin-like superfamily / Special / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha 類似検索 - ドメイン・相同性
NanoNextNL of the Government of the Netherlands and 130 partners
HTS&M Initiative: FES-0901;
オランダ
Biotechnology and Biological Sciences Research Council
BB/G015236/1
英国
The Netherlands Organization for Scientific Research
NWO grant: 016.072.321
オランダ
Brazilian science foundation
CNPq-152746/2012-9
ブラジル
Brazilian science foundation
CNPq-400796/2012-0
ブラジル
引用
ジャーナル: IUCrJ / 年: 2017 タイトル: Single-particle cryo-EM using alignment by classification (ABC): the structure of haemoglobin. 著者: Pavel 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 / 要旨: 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 ...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.