+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6043 | |||||||||
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タイトル | Structure of the Head of Bacteriophage Basilisk to 18 Angstrom resolution | |||||||||
マップデータ | Reconstruction of Basilisk Bacteriophage Head | |||||||||
試料 |
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キーワード | bacteriophage (ファージ) / icosahedron (二十面体) / triangulation number / T=9 / capsid (カプシド) / siphovirus / HK97 fold / Bacillus cereus (セレウス菌) | |||||||||
生物種 | Bacillus phage Basilisk (ファージ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / ネガティブ染色法 / 解像度: 18.0 Å | |||||||||
データ登録者 | Grose JH / Belnap DM / Jensen JD / Mathis AD / Prince JT / Merrill B / Burnett SH / Breakwell DP | |||||||||
引用 | ジャーナル: J Virol / 年: 2014 タイトル: The genomes, proteomes, and structures of three novel phages that infect the Bacillus cereus group and carry putative virulence factors. 著者: Julianne H Grose / David M Belnap / Jordan D Jensen / Andrew D Mathis / John T Prince / Bryan D Merrill / Sandra H Burnett / Donald P Breakwell / 要旨: This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. ...This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to well-characterized phages suggested that JL and Shanette were members of the family Myoviridae, which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T=9 icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus, B. anthracis, and B. thuringiensis. This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. Importance: The Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus, B. anthracis, and B. thuringiensis. Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_6043.map.gz | 69.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6043-v30.xml emd-6043.xml | 10.4 KB 10.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6043.tif | 767.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6043 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6043 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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-マップ
ファイル | ダウンロード / ファイル: emd_6043.map.gz / 形式: CCP4 / 大きさ: 137 MB / タイプ: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of Basilisk Bacteriophage Head | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : Bacteriophage Basilisk Head
全体 | 名称: Bacteriophage Basilisk Head |
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要素 |
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-超分子 #1000: Bacteriophage Basilisk Head
超分子 | 名称: Bacteriophage Basilisk Head / タイプ: sample / ID: 1000 / 集合状態: icosahedral / Number unique components: 1 |
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-超分子 #1: Bacillus phage Basilisk
超分子 | 名称: Bacillus phage Basilisk / タイプ: virus / ID: 1 / Name.synonym: Bacteriophage Basilisk, Basilisk Phage 詳細: Bacteriophage Basilisk head component (NCBI taxonomy ID 1296654) 生物種: Bacillus phage Basilisk / データベース: NCBI / ウイルスタイプ: VIRION / ウイルス・単離状態: SPECIES / ウイルス・エンベロープ: No / ウイルス・中空状態: No / Syn species name: Bacteriophage Basilisk, Basilisk Phage |
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宿主 | 生物種: Bacillus cereus (セレウス菌) / 株: BC7003 / 別称: BACTERIA(EUBACTERIA) |
ウイルス殻 | Shell ID: 1 / 名称: capsid / 直径: 780 Å / T番号(三角分割数): 9 |
-実験情報
-構造解析
手法 | ネガティブ染色法, クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | 詳細: PBS (phosphate-buffered saline) |
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染色 | タイプ: NEGATIVE / 詳細: no stain used |
グリッド | 詳細: holey carbon film (randomly sized holes) on copper grid |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK II 詳細: Blotting chamber (and sample) was maintained at 4 degrees Celsius before plunging; sample was applied with cold pipette tips. Humidity was 81-89%. 手法: blotted 1-2 seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
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電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 31400 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / 最大 デフォーカス(公称値): 3.3 µm / 最小 デフォーカス(公称値): 0.0 µm / 倍率(公称値): 29000 |
試料ステージ | 試料ホルダー: nitrogen cooled / 試料ホルダーモデル: GATAN LIQUID NITROGEN |
日付 | 2014年2月14日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM デジタル化 - スキャナー: NIKON SUPER COOLSCAN 9000 デジタル化 - サンプリング間隔: 6.35 µm / 実像数: 20 / 平均電子線量: 4.4 e/Å2 / 詳細: 16-bit scanned images truncated to 8-bit / ビット/ピクセル: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
-画像解析
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 18.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: AUTO3DEM / 使用した粒子像数: 2085 |
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-原子モデル構築 1
初期モデル | PDB ID: |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |