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基本情報
登録情報 | データベース: PDB / ID: 2om3 | ||||||
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タイトル | High-resolution cryo-EM structure of Tobacco Mosaic Virus | ||||||
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![]() | VIRUS / protein-RNA complex / four-helical up-and-down bundle / HELICAL VIRUS | ||||||
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 / RNA / Capsid protein![]() | ||||||
生物種 | ![]() ![]() | ||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å | ||||||
![]() | Sachse, C. | ||||||
![]() | ![]() 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. | ||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 139.6 KB | 表示 | ![]() |
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-検証レポート
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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モデル数 | 5 |
対称性 | らせん対称: (回転対称性: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 49 / Rise per n subunits: 1.4076 Å / Rotation per n subunits: 22.0318 °) |
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要素
#1: RNA鎖 | 分子量: 958.660 Da / 分子数: 1 / 由来タイプ: 合成 |
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#2: タンパク質 | 分子量: 17505.426 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
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試料調製
構成要素 | 名称: Tobacco Mosaic Virus / タイプ: VIRUS 詳細: Helical Virus. Pitch of helix: 23 Angstrom, 49.02 subunits make up three complete turns. |
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ウイルスについての詳細 | ホストのカテゴリ: PLANTS / タイプ: VIRION |
天然宿主 | 生物種: Nicotiana tabacum |
緩衝液 | 名称: Phosphate (5mM EDTA) / pH: 7.4 / 詳細: Phosphate (5mM EDTA) |
試料 | 濃度: 2.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: Quantifoil grid |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 詳細: The sample was plunge-frozen at 4C. |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai F30 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F30 / 日付: 2005年11月22日 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 59000 X / 倍率(補正後): 60190 X / 最大 デフォーカス(公称値): 4 nm / 最小 デフォーカス(公称値): 1.5 nm / Cs: 2 mm |
試料ホルダ | 温度: 93 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 15 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
画像スキャン | デジタル画像の数: 6 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M |
放射波長 | 相対比: 1 |
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解析
EMソフトウェア |
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CTF補正 | 詳細: Phase correction and amplitude weighting adapted from Grigorieff 1998(after determination of CTF and specimen tilt) | ||||||||||||
3次元再構成 | 手法: Single-particel helical reconstruction / 解像度: 4.4 Å / ピクセルサイズ(公称値): 1.186 Å / ピクセルサイズ(実測値): 1.163 Å 倍率補正: Maximization of FSC (resolution range 4-10 Angstrom) with atomic model 詳細: SIRT algorithm implemented in the SPIDER processing package (command BP RP) 対称性のタイプ: HELICAL | ||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL Target criteria: Minimization of least-square difference between observed and calculated densities 詳細: METHOD--Torsion angle molecular dynamics REFINEMENT PROTOCOL--Real-space molecular dynamics | ||||||||||||
原子モデル構築 | PDB-ID: 2TMV Accession code: 2TMV / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化ステップ | サイクル: LAST
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