+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4a5q | ||||||
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タイトル | Crystal structure of the chitinase Chi1 fitted into the 3D structure of the Yersinia entomophaga toxin complex | ||||||
要素 | CHI1 | ||||||
キーワード | HYDROLASE / BACTERIAL TOXIN / INSECTICIDE | ||||||
機能・相同性 | 機能・相同性情報 chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region 類似検索 - 分子機能 | ||||||
生物種 | YERSINIA ENTOMOPHAGA (バクテリア) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 17 Å | ||||||
データ登録者 | Busby, J.N. / Landsberg, M.J. / Simpson, R.M. / Jones, S.A. / Hankamer, B. / Hurst, M.R.H. / Lott, J.S. | ||||||
引用 | ジャーナル: J Mol Biol / 年: 2012 タイトル: Structural analysis of Chi1 Chitinase from Yen-Tc: the multisubunit insecticidal ABC toxin complex of Yersinia entomophaga. 著者: Jason N Busby / Michael J Landsberg / Robert M Simpson / Sandra A Jones / Ben Hankamer / Mark R H Hurst / J Shaun Lott / 要旨: Yersinia entomophaga MH96 is a native New Zealand soil bacterium that secretes a large ABC-type protein toxin complex, Yen-Tc, similar to those produced by nematode-associated bacteria such as ...Yersinia entomophaga MH96 is a native New Zealand soil bacterium that secretes a large ABC-type protein toxin complex, Yen-Tc, similar to those produced by nematode-associated bacteria such as Photorhabdus luminescens. Y. entomophaga displays an exceptionally virulent pathogenic phenotype in sensitive insect species, causing death within 72 h of infection. Because of this phenotype, there is intrinsic interest in the mechanism of action of Yen-Tc, and it also has the potential to function as a novel class of biopesticide. We have identified genes that encode chitinases as part of the toxin complex loci in Y. entomophaga MH96, P. luminescens, Photorhabdus asymbiotica and Xenorhabdus nematophila. Furthermore, we have shown that the secreted toxin complex from Y. entomophaga MH96 includes two chitinases as an integral part of the complex, a feature not described previously in other ABC toxins and possibly related to the severe disease caused by this bacterium. We present here the structure of the Y. entomophaga MH96 Chi1 chitinase, determined by X-ray crystallography to 1.74 Å resolution, and show that a ring of five symmetrically arranged lobes on the surface of the Yen-Tc toxin complex structure, as determined by single-particle electron microscopy, provides a good fit to the Chi1 monomer. We also confirm that the isolated chitinases display endochitinase activity, as does the complete toxin complex. | ||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-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 | 4a5q.cif.gz | 484.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4a5q.ent.gz | 395.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4a5q.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 | 4a5q_validation.pdf.gz | 736.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4a5q_full_validation.pdf.gz | 783.4 KB | 表示 | |
XML形式データ | 4a5q_validation.xml.gz | 71 KB | 表示 | |
CIF形式データ | 4a5q_validation.cif.gz | 107.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a5q ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a5q | HTTPS FTP |
-関連構造データ
関連構造データ | 1978M 3oa5C 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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1 |
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-要素
#1: タンパク質 | 分子量: 60726.355 Da / 分子数: 5 / 由来タイプ: 組換発現 由来: (組換発現) YERSINIA ENTOMOPHAGA (バクテリア) 株: MH96\:\:9 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): ROSETTA2 / 参照: UniProt: B6A876, chitinase |
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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: INSECTICIDAL TC FROM YERSINIA ENTOMOPHAGA STRAIN MH96 (DELETION CONSTRUCT 9)(AKA YEN-TC K9) タイプ: COMPLEX 詳細: PARTICLES WERE SELECTED USING SEMI-AUTOMATED PARTICLE SELECTION ( SWARMPS, E2BOXER.PY) |
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緩衝液 | 名称: 25 MM TRIS, 130 MM NACL / pH: 7.5 / 詳細: 25 MM TRIS, 130 MM NACL |
試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO |
染色 | タイプ: NEGATIVE / 染色剤: uranyl formate |
試料支持 | 詳細: OTHER |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F30 / 日付: 2009年6月2日 |
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): 59000 X / 最大 デフォーカス(公称値): 950 nm / 最小 デフォーカス(公称値): 900 nm / Cs: 2 mm |
試料ホルダ | 温度: 295 K |
撮影 | 電子線照射量: 80 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
画像スキャン | デジタル画像の数: 300 |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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対称性 | 点対称性: C5 (5回回転対称) | ||||||||||||
3次元再構成 | 手法: CROSS-COMMON LINES, PROJECTION MATCHING / 解像度: 17 Å / 粒子像の数: 10604 詳細: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1978.(DEPOSITION ID: 10324). 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | B value: 22.09 / プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Cross-correlation coefficient / 詳細: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||||||||||
原子モデル構築 | PDB-ID: 3OA5 Accession code: 3OA5 / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化 | 最高解像度: 17 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 17 Å
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