+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3nb3 | ||||||
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タイトル | The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components | ||||||
要素 |
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キーワード | MEMBRANE PROTEIN / virus assembly / cementing protein / bacteriophage / Sf6 / Shigella / beta-barrel / outer membrane protein / icosahedral | ||||||
機能・相同性 | 機能・相同性情報 outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / monoatomic ion transmembrane transport / cell outer membrane / virus receptor activity / outer membrane-bounded periplasmic space / receptor-mediated virion attachment to host cell / symbiont entry into host cell / DNA damage response / identical protein binding / membrane / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | Escherichia coli (大腸菌) | ||||||
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: 19 Å | ||||||
データ登録者 | Zhao, H. / Sequeira, R.D. / Galeva, N.A. / Tang, L. | ||||||
引用 | ジャーナル: Virology / 年: 2011 タイトル: The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion. 著者: Haiyan Zhao / Reuben D Sequeira / Nadezhda A Galeva / Liang Tang / 要旨: Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two ...Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol.Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state. | ||||||
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 | 3nb3.cif.gz | 159.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3nb3.ent.gz | 119.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3nb3.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nb3 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nb3 | HTTPS FTP |
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-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: (シェーンフリース記号: I (正20面体型対称)) |
詳細 | CHAIN C IS LOCATED ON AN ICOSAHEDRAL 2-FOLD AXIS AND HAS 0.50 OCCUPANCY. CHAIN D IS LOCATED ON AN ICOSAHEDRAL 3-FOLD AXIS AND HAS 0.33 OCCUPANCY. |
-要素
#1: タンパク質 | 分子量: 37272.672 Da / 分子数: 3 / 断片: outer membrane protein A / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P0A910 #2: タンパク質 | | 分子量: 38336.242 Da / 分子数: 1 / 断片: outer membrane protein C / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: K12 / 参照: UniProt: P06996 配列の詳細 | AUTHORS STATE THAT THE SEQUENCE CONFLICTS ARE INHERITED FROM IN THE ORIGINAL PDB ENTRY 1QJP USED FOR FITTING. | |
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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: bacteriophage Sf6 / タイプ: VIRUS / 別称: Sf6 |
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分子量 | 値: 19.2 MDa / 実験値: NO |
ウイルスについての詳細 | ホストのカテゴリ: GRAM-NEGATIVE BACTERIA / 単離: SPECIES / タイプ: VIRION |
天然宿主 | 生物種: Shigella flexneri |
ウイルス殻 | 名称: gp5 / 直径: 680 nm / 三角数 (T数): 7 |
緩衝液 | 名称: 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 / pH: 7.4 / 詳細: 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2 |
試料 | 濃度: 2 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: 300 mesh holey copper grids |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE 詳細: Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged ...詳細: Vitrification was carried out with a standard cryoEM method. The sample of 4 microlitres was applied to a holey EM grid, blotted for 3-4 seconds with a Whatman #2 filter paper, and plunged into ethane slush incubated in liquid nitrogen. The grid was stored in liquid nitrogen. |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 / 日付: 2008年7月18日 |
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): 39000 X / 最大 デフォーカス(公称値): 471 nm / 最小 デフォーカス(公称値): 1060 nm / Cs: 4 mm |
試料ホルダ | 温度: 89 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: GENERIC CCD (2k x 2k) |
-解析
CTF補正 | 詳細: none | |||||||||||||||||||||
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対称性 | 点対称性: I (正20面体型対称) | |||||||||||||||||||||
3次元再構成 | 手法: model-based projection / 解像度: 19 Å / 粒子像の数: 3232 / ピクセルサイズ(公称値): 4.05 Å / ピクセルサイズ(実測値): 3.9284 Å / 倍率補正: none 詳細: The initial model was the cryoEM map of the related phage P22. 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 詳細: METHOD--manual fitting in O coupled with local optimization with UCSF Chimera REFINEMENT PROTOCOL--rigid body | |||||||||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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