+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7x5k | ||||||
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タイトル | Tir-dsDNA complex, the initial binding state | ||||||
要素 |
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キーワード | HYDROLASE/DNA / plant innate immune receptor / nucleic acids / 2' / 3'cNMP / HYDROLASE-DNA COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 induction of programmed cell death / NADP catabolic process / cGMP biosynthetic process / NAD catabolic process / cAMP biosynthetic process / DNA catabolic process / RNA catabolic process / cAMP binding / ADP binding / defense response ...induction of programmed cell death / NADP catabolic process / cGMP biosynthetic process / NAD catabolic process / cAMP biosynthetic process / DNA catabolic process / RNA catabolic process / cAMP binding / ADP binding / defense response / double-stranded RNA binding / double-stranded DNA binding / hydrolase activity / signal transduction 類似検索 - 分子機能 | ||||||
生物種 | DNA molecule (その他) Linum usitatissimum (アマ) | ||||||
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: 3.8 Å | ||||||
データ登録者 | Tan, Y. / Xu, C. / Yu, D. / Song, W. / Wu, B. / Schulze-Lefert, P. / Chai, J. | ||||||
資金援助 | シンガポール, 1件
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引用 | ジャーナル: Cell / 年: 2022 タイトル: TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death. 著者: Dongli Yu / Wen Song / Eddie Yong Jun Tan / Li Liu / Yu Cao / Jan Jirschitzka / Ertong Li / Elke Logemann / Chenrui Xu / Shijia Huang / Aolin Jia / Xiaoyu Chang / Zhifu Han / Bin Wu / Paul ...著者: Dongli Yu / Wen Song / Eddie Yong Jun Tan / Li Liu / Yu Cao / Jan Jirschitzka / Ertong Li / Elke Logemann / Chenrui Xu / Shijia Huang / Aolin Jia / Xiaoyu Chang / Zhifu Han / Bin Wu / Paul Schulze-Lefert / Jijie Chai / 要旨: 2',3'-cAMP is a positional isomer of the well-established second messenger 3',5'-cAMP, but little is known about the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). ...2',3'-cAMP is a positional isomer of the well-established second messenger 3',5'-cAMP, but little is known about the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have the NADase function necessary but insufficient to activate plant immune responses. Here, we show that plant TIR proteins, besides being NADases, act as 2',3'-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data show that a TIR domain adopts distinct oligomers with mutually exclusive NADase and synthetase activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana (Nb), supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7, displays 2',3'-cAMP/cGMP but not 3',5'-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in Nb. Our study identifies a family of 2',3'-cAMP/cGMP synthetases and establishes a critical role for them in plant immune responses. | ||||||
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 | 7x5k.cif.gz | 564.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7x5k.ent.gz | 465.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7x5k.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 | 7x5k_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7x5k_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 7x5k_validation.xml.gz | 93.2 KB | 表示 | |
CIF形式データ | 7x5k_validation.cif.gz | 122 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/x5/7x5k ftp://data.pdbj.org/pub/pdb/validation_reports/x5/7x5k | 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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-要素
#1: DNA鎖 | 分子量: 13215.611 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Residues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 4.53. This out of range distance is due to an ...詳細: Residues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 4.53. This out of range distance is due to an intermediate state of a dsDNA hydrolysis process. Likewise, for the same reason, out of range distances are shown at the same position of chain Q. 由来: (組換発現) DNA molecule (その他) / 発現宿主: synthetic construct (人工物) #2: DNA鎖 | 分子量: 13242.652 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Residues DA E 12 and DT E 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 3.89. This out of range distance is due to an ...詳細: Residues DA E 12 and DT E 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 3.89. This out of range distance is due to an intermediate state of a dsDNA hydrolysis process. Likewise, for the same reason, out of range distances are shown at the same position of chain S. 由来: (組換発現) DNA molecule (その他) / 発現宿主: synthetic construct (人工物) #3: タンパク質 | 分子量: 23532.344 Da / 分子数: 16 / Mutation: E197G / 由来タイプ: 組換発現 / 詳細: L7 Tir domain / 由来: (組換発現) Linum usitatissimum (アマ) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9XEH4 構成要素の詳細 | Residues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly ...Residues DA B 12 and DT B 13 that are next to each other in the sample sequence are not properly linked: distance between O3' and P is 4.53. This out of range distance is due to an intermediate state of a dsDNA hydrolysis process. Likewise, for the same reason, out of range distances are shown at the same position of chain E, Q and S. | |
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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: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 |
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分子量 | 値: 20 kDa/nm / 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: 7 | ||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
急速凍結 | 凍結剤: METHANE |
-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 |
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 / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1000 nm / アライメント法: BASIC |
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 | 電子線照射量: 60 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.18rc5_3822: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア | 名称: RELION / バージョン: 3.08 / カテゴリ: 3次元再構成 | ||||||||||||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
らせん対称 | 回転角度/サブユニット: 159.2 ° / 軸方向距離/サブユニット: 16.56 Å / らせん対称軸の対称性: C1 | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 228796 / 対称性のタイプ: HELICAL | ||||||||||||||||||||||||
原子モデル構築 | B value: 215 / プロトコル: RIGID BODY FIT / 空間: REAL | ||||||||||||||||||||||||
拘束条件 |
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