+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5m3l | |||||||||||||||||||||
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タイトル | Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin | |||||||||||||||||||||
要素 |
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キーワード | OXYGEN TRANSPORT / Lumbricus terrestris / hemoglobin / oxygen carrier / erythrocruorin | |||||||||||||||||||||
機能・相同性 | 機能・相同性情報 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 | |||||||||||||||||||||
生物種 | Lumbricus terrestris (無脊椎動物) | |||||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | |||||||||||||||||||||
データ登録者 | 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. | |||||||||||||||||||||
資金援助 | オランダ, 英国, ブラジル, 6件
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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. | |||||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5m3l.cif.gz | 490.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5m3l.ent.gz | 395.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5m3l.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 5m3l_validation.pdf.gz | 2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5m3l_full_validation.pdf.gz | 2 MB | 表示 | |
XML形式データ | 5m3l_validation.xml.gz | 83.4 KB | 表示 | |
CIF形式データ | 5m3l_validation.cif.gz | 116.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3l ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3l | HTTPS FTP |
-関連構造データ
-リンク
-集合体
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対称性 | 点対称性: (シェーンフリース記号: D6 (2回x6回 2面回転対称)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: _ / Refine code: _
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