+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-1213 | |||||||||
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タイトル | Structural model for the mannose receptor family uncovered by electron microscopy of Endo180 and the mannose receptor. | |||||||||
マップデータ | This a 3D reconstruction of the soluble fragment of the mannose receptor | |||||||||
試料 |
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生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 33.0 Å | |||||||||
データ登録者 | Boskovic J / Arnold JN / Stilion R / Gordon S / Sim RB / Rivera-Calzada A / Wienke D / Isacke CM / Martinez-Pomares L / Llorca O | |||||||||
引用 | ジャーナル: J Biol Chem / 年: 2006 タイトル: Structural model for the mannose receptor family uncovered by electron microscopy of Endo180 and the mannose receptor. 著者: Jasminka Boskovic / James N Arnold / Richard Stilion / Siamon Gordon / Robert B Sim / Angel Rivera-Calzada / Dirk Wienke / Clare M Isacke / Luisa Martinez-Pomares / Oscar Llorca / 要旨: The mannose receptor family comprises four members in mammals, Endo180 (CD280), DEC-205 (CD205), phospholipase A(2) receptor (PLA(2)R) and the mannose receptor (MR, CD206), whose extracellular ...The mannose receptor family comprises four members in mammals, Endo180 (CD280), DEC-205 (CD205), phospholipase A(2) receptor (PLA(2)R) and the mannose receptor (MR, CD206), whose extracellular portion contains a similar domain arrangement: an N-terminal cysteine-rich domain (CysR) followed by a single fibronectin type II domain (FNII) and 8-10 C-type lectin-like domains (CTLDs). These proteins mediate diverse functions ranging from extracellular matrix turnover through collagen uptake to homeostasis and immunity based on sugar recognition. Endo180 and the MR are multivalent transmembrane receptors capable of interacting with multiple ligands; in both receptors FNII recognizes collagens, and a single CTLD retains lectin activity (CTLD2 in Endo180 and CTLD4 in MR). It is expected that the overall conformation of these multivalent molecules would deeply influence their function as the availability of their binding sites could be altered under different conditions. However, conflicting reports have been published on the three-dimensional arrangement of these receptors. Here, we have used single particle electron microscopy to elucidate the three-dimensional organization of the MR and Endo180. Strikingly, we have found that both receptors display distinct three-dimensional structures, which are, however, conceptually very similar: a bent and compact conformation built upon interactions of the CysR domain and the lone functional CTLD. Biochemical and electron microscopy experiments indicate that, under a low pH mimicking the endosomal environment, both MR and Endo180 experience large conformational changes. We propose a structural model for the mannose receptor family where at least two conformations exist that may serve to regulate differences in ligand selectivity. | |||||||||
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_1213.map.gz | 216.2 KB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-1213-v30.xml emd-1213.xml | 10.7 KB 10.7 KB | 表示 表示 | EMDBヘッダ |
画像 | 1213.gif | 39.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-1213 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1213 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_1213_validation.pdf.gz | 209.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_1213_full_validation.pdf.gz | 208.7 KB | 表示 | |
XML形式データ | emd_1213_validation.xml.gz | 5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1213 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1213 | 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_1213.map.gz / 形式: CCP4 / 大きさ: 422.9 KB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | This a 3D reconstruction of the soluble fragment of the mannose receptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 5.3 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 : Soluble Form of Mouse Mannose Receptor
全体 | 名称: Soluble Form of Mouse Mannose Receptor |
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要素 |
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-超分子 #1000: Soluble Form of Mouse Mannose Receptor
超分子 | 名称: Soluble Form of Mouse Mannose Receptor / タイプ: sample / ID: 1000 / 集合状態: monomer / Number unique components: 1 |
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分子量 | 実験値: 160 KDa / 理論値: 180 KDa / 手法: Gel Filtration Chromatography |
-分子 #1: Mannose Receptor
分子 | 名称: Mannose Receptor / タイプ: protein_or_peptide / ID: 1 / Name.synonym: MR 詳細: MR(CD206) is a member of mannose receptor family of transmembrane receptors which acts as a molecular scavenger that binds and internalises potentially harmful glycoproteins and may also ...詳細: MR(CD206) is a member of mannose receptor family of transmembrane receptors which acts as a molecular scavenger that binds and internalises potentially harmful glycoproteins and may also mediate phagocytosis of a wide variety of microbes. コピー数: 1 / 集合状態: Monomer / 組換発現: Yes |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) / 別称: Mouse / Organelle: Supernatant / 細胞中の位置: membrane |
分子量 | 実験値: 180 KDa / 理論値: 160 KDa |
組換発現 | 生物種: 293T / 組換プラスミド: pMH |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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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 | 0.2 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: 10mMTris,140mM Nacl,10 mM CaCl2 |
染色 | タイプ: NEGATIVE 詳細: Protein was adsorbed to glow-discharged carbon-coated grids and negatively stained with 2% w/v uranyl acetate |
グリッド | 詳細: 400 mesh copper-rhodium grid |
凍結 | 凍結剤: NONE |
-電子顕微鏡法
顕微鏡 | JEOL 1230 |
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アライメント法 | Legacy - 非点収差: objective lens astigmatism was corrected at 100,000 times magnification |
詳細 | Electron microscope was JEOL JEM-120, 120kV. Specimen holder, JEOL type M: 207EM-11020. Images were colected in low-dose conditions |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK 4489 FILM / デジタル化 - スキャナー: OTHER / デジタル化 - サンプリング間隔: 5.3 µm / 詳細: Minolta Dimage Scan Multi Pro. Scan at 2400 dpi / ビット/ピクセル: 16 |
電子線 | 加速電圧: 100 kV / 電子線源: TUNGSTEN HAIRPIN |
電子光学系 | 倍率(補正後): 38000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.9 mm / 倍率(公称値): 40000 |
試料ステージ | 試料ホルダー: Eucentric / 試料ホルダーモデル: OTHER |
-画像解析
詳細 | Particles were selected using boxer program from EMAN (J.Struct.Biol. (1999) 128:82-97) |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 33.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: EMAN 詳細: Angular refinement using a blob as starting reference volume 使用した粒子像数: 7322 |