+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8b14 | |||||||||
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タイトル | T5 Receptor Binding Protein pb5 in complex with its E. coli receptor FhuA | |||||||||
要素 |
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キーワード | VIRAL PROTEIN / bacteriophage / receptor / complex / RPB | |||||||||
機能・相同性 | 機能・相同性情報 siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virus tail / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell ...siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virus tail / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / iron ion binding / protein domain specific binding / membrane 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) Escherichia phage T5 (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: 2.6 Å | |||||||||
データ登録者 | Degroux, S. / Effantin, G. / Linares, R. / Schoehn, G. / Breyton, C. | |||||||||
資金援助 | フランス, 2件
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引用 | ジャーナル: J Virol / 年: 2023 タイトル: Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger. 著者: Séraphine Degroux / Grégory Effantin / Romain Linares / Guy Schoehn / Cécile Breyton / 要旨: Bacteriophages, viruses infecting bacteria, recognize their host with high specificity, binding to either saccharide motifs or proteins of the cell wall of their host. In the majority of ...Bacteriophages, viruses infecting bacteria, recognize their host with high specificity, binding to either saccharide motifs or proteins of the cell wall of their host. In the majority of bacteriophages, this host recognition is performed by receptor binding proteins (RBPs) located at the extremity of a tail. Interaction between the RBPs and the host is the trigger for bacteriophage infection, but the molecular details of the mechanisms are unknown for most bacteriophages. Here, we present the electron cryomicroscopy (cryo-EM) structure of bacteriophage T5 RBP in complex with its Escherichia coli receptor, the iron ferrichrome transporter FhuA. Monomeric RBP is located at the extremity of T5's long flexible tail, and its irreversible binding to FhuA commits T5 to infection. Analysis of the structure of RBP within the complex, comparison with its AlphaFold2-predicted structure, and its fit into a previously determined map of the T5 tail tip in complex with FhuA allow us to propose a mechanism of transmission of the RBP receptor binding to the straight fiber, initiating the cascade of events that commits T5 to DNA ejection. Tailed bacteriophages specifically recognize their bacterial host by interaction of their receptor binding protein(s) (RBPs) with saccharides and/or proteins located at the surface of their prey. This crucial interaction commits the virus to infection, but the molecular details of this mechanism are unknown for the majority of bacteriophages. We determined the structure of bacteriophage T5 RBP in complex with its E. coli receptor, FhuA, by cryo-EM. This first structure of an RBP bound to its protein receptor allowed us to propose a mechanism of transmission of host recognition to the rest of the phage, ultimately opening the capsid and perforating the cell wall and, thus, allowing safe channeling of the DNA into the host cytoplasm. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8b14.cif.gz | 439.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8b14.ent.gz | 363.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8b14.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 | 8b14_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8b14_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 8b14_validation.xml.gz | 55.3 KB | 表示 | |
CIF形式データ | 8b14_validation.cif.gz | 82.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/b1/8b14 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/8b14 | HTTPS FTP |
-関連構造データ
関連構造データ | 15802MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 79876.945 Da / 分子数: 1 変異: Presence of an Histag after P405, added residues : SHHHHHHGS 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): AW740 / 参照: UniProt: P06971 |
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#2: タンパク質 | 分子量: 68782.562 Da / 分子数: 1 / 変異: Presence of an Histag in C-ter position / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia phage T5 (ファージ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P23207 |
#3: 化合物 | ChemComp-DDQ / |
#4: 化合物 | ChemComp-LU9 / [( |
研究の焦点であるリガンドがあるか | Y |
-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 |
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分子量 | 値: 0.15 MDa / 実験値: NO | ||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 8.5 | ||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 1.1111111111111 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: The FhuA-pb5 complex was formed by adding equimolar amounts of the two proteins, which results in 100% complex formation. FhuA-RBPpb5 complex is stabilized with 1.6% C10DAO at a protein concentration of 4.3 mg/ml | ||||||||||||||||||||||||||||
試料支持 | 詳細: 25 mA / グリッドの材料: COPPER/RHODIUM / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R2/1 | ||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 293.15 K 詳細: 3.5 microliters of the FhuA-pb5 complex were deposited on a freshly glow discharged (25 mA, 30 sec) Cu/Rh 400 mesh Quantifoil R 2/1 EM grids and flash-frozen in nitrogen-cooled liquid ethane ...詳細: 3.5 microliters of the FhuA-pb5 complex were deposited on a freshly glow discharged (25 mA, 30 sec) Cu/Rh 400 mesh Quantifoil R 2/1 EM grids and flash-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100% humidity, 293.15K, 2s blotting time, blot force 1). |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company | ||||||||||||
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顕微鏡 | モデル: FEI TITAN KRIOS / 詳細: calibrated pixel size = 1.052 | ||||||||||||
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM | ||||||||||||
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 2600 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2.7 mm / アライメント法: COMA FREE | ||||||||||||
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||
撮影 | Imaging-ID: 1 / 電子線照射量: 60 e/Å2 / 検出モード: COUNTING / フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) / 撮影したグリッド数: 1
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電子光学装置 | エネルギーフィルター名称: GIF Quantum LS / エネルギーフィルタースリット幅: 20 eV | ||||||||||||
画像スキャン |
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-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 2191586 | ||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 109350 / アルゴリズム: BACK PROJECTION / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL / 空間: REAL 詳細: The pb5 protein model was built de novo in the cryo-electron microscopy map. FhuA was adapted from the FhuA structure solved by X-ray crystallography (PDB 2GRX). The two structures were first ...詳細: The pb5 protein model was built de novo in the cryo-electron microscopy map. FhuA was adapted from the FhuA structure solved by X-ray crystallography (PDB 2GRX). The two structures were first refined separately using Coot (version 0.9.2) and Phenix (version 1.18.2-3874) softwares, then together. Structure validation was done using MolProbity. | ||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 2GRX Accession code: 2GRX / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||||||||||
拘束条件 |
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