+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-1598 | |||||||||
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タイトル | Cryo-negative staining electron microscopy reveals the structure and oligomeric state of Limulus SAP-like pentraxin | |||||||||
マップデータ | This is the volume of Lumulus Serum Amyloid P-Component | |||||||||
試料 |
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キーワード | Limulus / pentraxin / serum amyloid p component / phosphoethanolamine binding (エタノールアミンリン酸) / cryoEM (低温電子顕微鏡法) | |||||||||
機能・相同性 | Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily / extracellular region / metal ion binding / Pentraxin family member 機能・相同性情報 | |||||||||
生物種 | Limulus polyphemus (カブトガニ) | |||||||||
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: 14.0 Å | |||||||||
データ登録者 | Shrive AK / Burns I / Chou HT / Stahlberg H / Armstrong PB / Greenhough TJ | |||||||||
引用 | ジャーナル: J Mol Biol / 年: 2009 タイトル: Crystal structures of Limulus SAP-like pentraxin reveal two molecular aggregations. 著者: Annette K Shrive / Ian Burns / Hui-Ting Chou / Henning Stahlberg / Peter B Armstrong / Trevor J Greenhough / 要旨: The serum-amyloid-P-component-like pentraxin from Limulus polyphemus, a recently discovered pentraxin species and important effector protein of the hemolymph immune system, displays two distinct ...The serum-amyloid-P-component-like pentraxin from Limulus polyphemus, a recently discovered pentraxin species and important effector protein of the hemolymph immune system, displays two distinct doubly stacked cyclic molecular aggregations, heptameric and octameric. The refined three-dimensional structures determined by X-ray crystallography, both based on the same cDNA sequence, show that each aggregate is constructed from a similar dimer of protomers, which is repeated to make up the ring structure. The native octameric form has been refined at a resolution of 3 A, the native heptameric form at 2.3 A, and the phosphoethanolamine (PE)-bound octameric form at 2.7 A. The existence of the hitherto undescribed heptameric form was confirmed by single-particle analysis using cryo-electron microscopy. In the native structures, the calcium-binding site is similar to that in human pentraxins, with two calcium ions bound in each subunit. Upon binding PE, however, each subunit binds a third calcium ion, with all three calcium ions contributing to the binding and orientation of the bound phosphate group within the ligand-binding pocket. While the phosphate is well-defined in the electron density, the ethanolamine group is poorly defined, suggesting structural and binding variabilities of this group. Although sequence homology with human serum amyloid P component is relatively low, structural homology is high, with very similar overall folds and a common affinity for PE. This is due, in part, to a "topological" equivalence of side-chain position. Identical side chains that are important in both function and fold, from different regions of the sequence in human and Limulus structures, occupy similar space within the overall subunit fold. Sequence and structure alignment, based on the refined three-dimensional structures presented here and the known horseshoe crab pentraxin sequences, suggest that adaptation and refinement of C-reactive-protein-mediated immune responses in these ancient creatures lacking antibody-based immunity are based on adaptation by gene duplication. | |||||||||
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_1598.map.gz | 12 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-1598-v30.xml emd-1598.xml | 8.9 KB 8.9 KB | 表示 表示 | EMDBヘッダ |
画像 | 1598.gif | 57.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-1598 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1598 | 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_1598.map.gz / 形式: CCP4 / 大きさ: 15.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | This is the volume of Lumulus Serum Amyloid P-Component | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.25 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 : Limulus SAP-like pentraxin
全体 | 名称: Limulus SAP-like pentraxin |
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要素 |
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-超分子 #1000: Limulus SAP-like pentraxin
超分子 | 名称: Limulus SAP-like pentraxin / タイプ: sample / ID: 1000 集合状態: Limulus SAP-like pentraxin comprises 14 protomers packed as a doubly stacked ring Number unique components: 1 |
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分子量 | 理論値: 300 KDa |
-分子 #1: SAP-like pentraxin
分子 | 名称: SAP-like pentraxin / タイプ: protein_or_peptide / ID: 1 / Name.synonym: SAP-like pentraxin / コピー数: 14 / 集合状態: 14-mer / 組換発現: No |
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由来(天然) | 生物種: Limulus polyphemus (カブトガニ) / 別称: Atlantic horseshoe crab / 組織: hemolymph |
分子量 | 理論値: 300 KDa |
-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
濃度 | 0.1 mg/mL |
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緩衝液 | pH: 7 / 詳細: 0.1M citrate |
染色 | タイプ: NEGATIVE 詳細: 3ul protein sample laied on the grid for 30 seconds and the grid floated on saturated ammonium molybdate for 1 minute |
グリッド | 詳細: 400 mesh quantifoil grid |
凍結 | 凍結剤: ETHANE / チャンバー内温度: 100 K / 装置: OTHER 手法: The grid was blotted for 6 seconds and air-dried for 3 seconds before plunging |
-電子顕微鏡法
顕微鏡 | JEOL 2100F |
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電子線 | 加速電圧: 120 kV / 電子線源: LAB6 |
電子光学系 | 倍率(補正後): 80000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 80000 |
試料ステージ | 試料ホルダー: side entry Gatan 626 / 試料ホルダーモデル: GATAN LIQUID NITROGEN |
温度 | 平均: 95 K |
詳細 | Imaged in JEOL minimum dose system |
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: PRIMESCAN / デジタル化 - サンプリング間隔: 10 µm / 実像数: 18 / ビット/ピクセル: 16 |
-画像解析
最終 再構成 | 想定した対称性 - 点群: D7 (2回x7回 2面回転対称) アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 14.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: SPIDER / 詳細: D7 symmetry was imposed on the reconstruction / 使用した粒子像数: 12243 |
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詳細 | The particles were selected automatically by the program BOXER and screened manually |