+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1yxn | ||||||
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タイトル | Pseudo-atomic model of a fiberless isometric variant of bacteriophage phi29 | ||||||
要素 | Major head protein | ||||||
キーワード | VIRUS / phi29 / capsid / icosahedral virus capsid / hk97 fold / phage / bacterial immuno-globulin / BIG2 / Icosahedral virus | ||||||
生物種 | Bacillus phage phi29 (ファージ) | ||||||
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: 7.9 Å | ||||||
データ登録者 | Morais, M.C. / Choi, K.H. / Koti, J.S. / Chipman, P.R. / Anderson, D.L. / Rossmann, M.G. | ||||||
引用 | ジャーナル: Mol Cell / 年: 2005 タイトル: Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29. 著者: Marc C Morais / Kyung H Choi / Jaya S Koti / Paul R Chipman / Dwight L Anderson / Michael G Rossmann / 要旨: Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been ...Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been determined to 7.9 A resolution by cryo-electron microscopy (cryo-EM), allowing the identification of alpha helices and beta sheets. Their arrangement indicates that the folds of the phi29 and bacteriophage HK97 capsid proteins are similar except for an additional immunoglobulin-like domain of the phi29 protein. An atomic model that incorporates these two domains fits well into the cryo-EM density of the T = 3, fiberless isometric phi29 particle, and cryo-EM structures of fibered isometric and fiberless prolate prohead phi29 particles at resolutions of 8.7 A and 12.7 A, respectively. Thus, phi29 joins the growing number of phages that utilize the HK97 capsid structure, suggesting that this protein fold may be as prevalent in capsids of dsDNA phages as the jelly roll fold is in eukaryotic viruses. | ||||||
履歴 |
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Remark 999 | SEQUENCE The authors state that an alignment between the coordinate C-alpha atoms and the sequence ...SEQUENCE The authors state that an alignment between the coordinate C-alpha atoms and the sequence is not possible. The following is the one-letter sequence for the protein modeled in this structure, SwissProt entry P13849: MRITFNDVKTSLGITESYDIVNAIRNSQGDNFKSYVPLATANNVAEVGAGILINQTVQND FITSLVDRIGLVVIRQVSLNNPLKKFKKGQIPLGRTIEEIYTDITKEKQYDAEEAEQKVF EREMPNVKTLFHERNRQGFYHQTIQDDSLKTAFVSWGNFESFVSSIINAIYNSAEVDEYE YMKLLVDNYYSKGLFTTVKIDEPTSSTGALTEFVKKMRATARKLTLPQGSRDWNSMAVRT RSYMEDLHLIIDADLEAELDVDVLAKAFNMNRTDFLGNVTVIDGFASTGLEAVLVDKDWF MVYDNLHKMETVRNPRGLYWNYYYHVWQTLSVSRFANAVAFVSGDVPAVTQVIVSPNIAA VKQGGQQQFTAYVRATNAKDHKVVWSVEGGSTGTAITGDGLLSVSGNEDNQLTVKATVDI GTEDKPKLVVGEAVVSIRPNNASGGAQA |
-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 | 1yxn.cif.gz | 37.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1yxn.ent.gz | 23.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1yxn.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 | 1yxn_validation.pdf.gz | 788.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1yxn_full_validation.pdf.gz | 787.7 KB | 表示 | |
XML形式データ | 1yxn_validation.xml.gz | 17 KB | 表示 | |
CIF形式データ | 1yxn_validation.cif.gz | 26.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/yx/1yxn ftp://data.pdbj.org/pub/pdb/validation_reports/yx/1yxn | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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対称性 | 点対称性: (ヘルマン・モーガン記号: 532 / シェーンフリース記号: I (正20面体型対称)) |
-要素
#1: タンパク質 | 分子量: 30655.668 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus phage phi29 (ファージ) / 属: Phi29-like viruses / 細胞株: phi29 / 遺伝子: 8 / 発現宿主: Bacillus subtilis (枯草菌) |
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-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: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Fiberless isometric phi29 capsid / タイプ: VIRUS 詳細: The capsid protein assembles a T=3 icosahedral virus shell. The virus particle is a protein shell with icosahedral symmetry. To generate the complete icosahedral particle, apply the following ...詳細: The capsid protein assembles a T=3 icosahedral virus shell. The virus particle is a protein shell with icosahedral symmetry. To generate the complete icosahedral particle, apply the following 59 matrices to the three chains in the icosahedral asymmetric unit, and combine with the original coordinates of the icosahedral asymmetric unit: 由来: NATURAL |
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由来(天然) | 生物種: Enterobacteria phage T4 (ファージ) |
ウイルスについての詳細 | ホストのカテゴリ: BACTERIA / タイプ: VIRION |
天然宿主 | 生物種: Bacillus subtilus |
緩衝液 | 名称: tris-HCL / pH: 7.8 / 詳細: tris-HCL |
試料 | 濃度: 1 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: electron microscopy grid - in vitreous ice |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 詳細: frozen in liquid ethane |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM200FEG/ST |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 38000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 700 nm / Cs: 2 mm |
試料ホルダ | 温度: 100 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Inverse of CTF was applied to images. Both phases and amplitudes were corrected. | ||||||||||||||||||||||||||||
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||||||||||||||||||
3次元再構成 | 手法: 3D reconstructions were calculated using the Fourier-Bessel method. Initial orientations were found via common-lines, improved using model based polar Fourier transform methods, and finally ...手法: 3D reconstructions were calculated using the Fourier-Bessel method. Initial orientations were found via common-lines, improved using model based polar Fourier transform methods, and finally refined by minimizing the vector difference between between structure factors calculated from a particle image and those from a central section of the Fourier transform of the model. 解像度: 7.9 Å / 粒子像の数: 5922 / ピクセルサイズ(公称値): 1.8421 Å 詳細: Software used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement. 対称性のタイプ: POINT | ||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL Target criteria: rigid body refinement in real space against laplacian filtered EM density, using the program COLORES in the package SITUS. Each molecule in the T=3 asymmetric unit was refined separately. 詳細: METHOD--6D search for each symmetry related molecule in the icosahedral asymmetric unit REFINEMENT PROTOCOL--rigid body | ||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST
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