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基本情報
登録情報 | データベース: PDB / ID: 8csl | ||||||
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タイトル | Sub-tomogram averaging of erythrocyte ankyrin-1 complex | ||||||
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![]() | TRANSPORT PROTEIN/STRUCTURAL PROTEIN / Membrane protein / ankyrin complex / TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex | ||||||
機能・相同性 | ![]() methylammonium transmembrane transport / Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) / Rhesus blood group biosynthesis / methylammonium transmembrane transporter activity / Rhesus glycoproteins mediate ammonium transport. / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / ammonium homeostasis / spectrin-associated cytoskeleton / hemoglobin metabolic process ...methylammonium transmembrane transport / Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) / Rhesus blood group biosynthesis / methylammonium transmembrane transporter activity / Rhesus glycoproteins mediate ammonium transport. / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / ammonium homeostasis / spectrin-associated cytoskeleton / hemoglobin metabolic process / positive regulation of organelle organization / protein-glutamine gamma-glutamyltransferase activity / maintenance of epithelial cell apical/basal polarity / leak channel activity / pH elevation / Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) / negative regulation of urine volume / NrCAM interactions / ammonium transmembrane transport / Neurofascin interactions / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex / plasma membrane phospholipid scrambling / CHL1 interactions / monoatomic anion transmembrane transporter activity / ammonium channel activity / chloride:bicarbonate antiporter activity / cytoskeletal anchor activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / M band / monoatomic anion transport / inorganic cation transmembrane transport / Interaction between L1 and Ankyrins / chloride transport / chloride transmembrane transporter activity / ankyrin binding / negative regulation of glycolytic process through fructose-6-phosphate / hemoglobin binding / spectrin binding / cortical cytoskeleton / erythrocyte maturation / exocytosis / axolemma / erythrocyte development / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / protein-membrane adaptor activity / spleen development / chloride transmembrane transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / Cell surface interactions at the vascular wall / regulation of intracellular pH / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cell morphogenesis / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / sarcolemma / transmembrane transport / multicellular organismal-level iron ion homeostasis / Z disc / blood coagulation / virus receptor activity / regulation of cell shape / ATPase binding / basolateral plasma membrane / protein phosphatase binding / postsynaptic membrane / transmembrane transporter binding / blood microparticle / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / protein homodimerization activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | 電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 25 Å | ||||||
![]() | Vallese, F. / Kim, K. / Yen, L.Y. / Johnston, J.D. / Noble, A.J. / Cali, T. / Clarke, O.B. | ||||||
資金援助 | 1件
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![]() | ![]() タイトル: Architecture of the human erythrocyte ankyrin-1 complex. 著者: Francesca Vallese / Kookjoo Kim / Laura Y Yen / Jake D Johnston / Alex J Noble / Tito Calì / Oliver Biggs Clarke / ![]() ![]() 要旨: The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association ...The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2, glycophorin A and glycophorin B. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and, unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 133.9 KB | 表示 | |
CIF形式データ | ![]() | 240.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 26965MC ![]() 7uz3C ![]() 7uzeC ![]() 7uzqC ![]() 7uzsC ![]() 7uzuC ![]() 7uzvC ![]() 7v07C ![]() 7v0kC ![]() 7v0mC ![]() 7v0qC ![]() 7v0sC ![]() 7v0tC ![]() 7v0uC ![]() 7v0xC ![]() 7v0yC ![]() 7v19C ![]() 8crqC ![]() 8crrC ![]() 8crtC ![]() 8cs9C ![]() 8csvC ![]() 8cswC ![]() 8csxC ![]() 8csyC ![]() 8ct2C ![]() 8ct3C ![]() 8cteC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
実験データセット #1 | データ参照: ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 7種, 19分子 AWVeYfZgKLQXPRaSbTc
#1: タンパク質 | 分子量: 206522.625 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() | ||||||||||
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#2: タンパク質 | 分子量: 101883.859 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) ![]() #3: タンパク質 | | 分子量: 45598.918 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() #4: タンパク質 | 分子量: 44229.629 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() #5: タンパク質 | | 分子量: 77096.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() #6: タンパク質 | | 分子量: 9789.674 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() #7: タンパク質 | 分子量: 16348.433 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-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: サブトモグラム平均法 |
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試料調製
構成要素 | 名称: Sub-tomogram average of ankyrin-1 complexes from native erythrocyte vesicles タイプ: COMPLEX / Entity ID: all / 由来: NATURAL |
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由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7.4 / 詳細: 130 mM KCl, 10 mM HEPES, pH 7.4 |
試料 | 濃度: 5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Ghost membranes (~100 mg) were pelleted (6,000 x g, 10 minutes), washed 5 times in 130 mM KCl, 10 mM HEPES, pH 7.4, and then homogenized with the same buffer. The sample was sonicated using ...詳細: Ghost membranes (~100 mg) were pelleted (6,000 x g, 10 minutes), washed 5 times in 130 mM KCl, 10 mM HEPES, pH 7.4, and then homogenized with the same buffer. The sample was sonicated using microprobe (amplitude = 30, pulse on = 5 sec, rest time = 10 sec, total pulse on = 50 sec). Large fragments are removed by centrifugation (6,000 x g, 10 minutes) and the supernatant was extruded (Avanti Polar Lipid) 10 times using a 400 nm filter. After extrusion, vesicles were collected by ultra-centrifugation at 35,000 rpm for 30 minutes (S120-AT3, Sorvall). The pellet, which contains vesicles, was resuspended at a final concentration of 5 mg/mL. All steps were performed at room temperature to facilitate vesicle formation. |
急速凍結 | 凍結剤: ETHANE |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 5000 nm / 最小 デフォーカス(公称値): 3000 nm / Cs: 0.01 mm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 3.14 e/Å2 / Avg electron dose per subtomogram: 113 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
電子光学装置 | エネルギーフィルタースリット幅: 20 eV |
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解析
EMソフトウェア |
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CTF補正 | 詳細: Warp / タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||
3次元再構成 | 解像度: 25 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 1596 / 対称性のタイプ: POINT | |||||||||
EM volume selection | 詳細: Picked using crYOLO, trained using manual picks. / Num. of tomograms: 100 / Num. of volumes extracted: 60029 | |||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT 詳細: Erythrocyte ankyrin-1 complex (Class1, 8CS9) was rigid fit as a single body to the map using fitmap in UCSF Chimera, after which waters, ligands and sidechains were removed from the model. | |||||||||
原子モデル構築 | PDB-ID: 8CS9 Accession code: 8CS9 / Source name: PDB / タイプ: experimental model |