- EMDB-1316: High-resolution electron microscopy of helical specimens: a fresh... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-1316
タイトル
High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
マップデータ
A 69 Angstrom section of the virus. The complete virus contains contains approximately 44 repeats of this 69 Angstrom section. The section contains 49 asymmetric units of the helical virus.Cube of 241 x 241 x 241 Angstrom
試料
試料: Tobacco Mosaic Virus
ウイルス: Tobacco mosaic virus (ウイルス)
機能・相同性
Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / Capsid protein
ジャーナル: J Mol Biol / 年: 2007 タイトル: High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus. 著者: Carsten Sachse / James Z Chen / Pierre-Damien Coureux / M Elizabeth Stroupe / Marcus Fändrich / Nikolaus Grigorieff / 要旨: The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be ...The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.
ダウンロード / ファイル: emd_1316.map.gz / 形式: CCP4 / 大きさ: 29.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
A 69 Angstrom section of the virus. The complete virus contains contains approximately 44 repeats of this 69 Angstrom section. The section contains 49 asymmetric units of the helical virus.Cube of 241 x 241 x 241 Angstrom
想定した対称性 - らせんパラメータ - 軸対称性: C1 (非対称) アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 4.4 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Spider 詳細: Final map was calculated from the central 241x241x241 cube.
CTF補正
詳細: CTFFIND and CTFTILT phase-correction and amplitude-weighting of each paritcle after Grigorieff 1998