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基本情報
登録情報 | データベース: PDB / ID: 3j08 | ||||||
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タイトル | High resolution helical reconstruction of the bacterial p-type ATPase copper transporter CopA | ||||||
![]() | copper-exporting P-type ATPase A | ||||||
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機能・相同性 | ![]() P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / intracellular copper ion homeostasis / copper ion binding / ![]() ![]() ![]() 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Wu, C. / Allen, G.S. / Cardozo, T. / Stokes, D.L. | ||||||
![]() | ![]() タイトル: The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking. 著者: Gregory S Allen / Chen-Chou Wu / Tim Cardozo / David L Stokes / ![]() 要旨: CopA uses ATP to pump Cu(+) across cell membranes. X-ray crystallography has defined atomic structures of several related P-type ATPases. We have determined a structure of CopA at 10 Å resolution ...CopA uses ATP to pump Cu(+) across cell membranes. X-ray crystallography has defined atomic structures of several related P-type ATPases. We have determined a structure of CopA at 10 Å resolution by cryo-electron microscopy of a new crystal form and used computational molecular docking to study the interactions between the N-terminal metal-binding domain (NMBD) and other elements of the molecule. We found that the shorter-chain lipids used to produce these crystals are associated with movements of the cytoplasmic domains, with a novel dimer interface and with disordering of the NMBD, thus offering evidence for the transience of its interaction with the other cytoplasmic domains. Docking identified a binding site that matched the location of the NMBD in our previous structure by cryo-electron microscopy, allowing a more detailed view of its binding configuration and further support for its role in autoinhibition. | ||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 216 KB | 表示 | ![]() |
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PDB形式 | ![]() | 168.6 KB | 表示 | ![]() |
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-関連構造データ
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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
#1: タンパク質 | 分子量: 69213.789 Da / 分子数: 2 / 断片: deltaC-CopA (UNP residues 93-737) / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() ![]() 遺伝子: copA, pacS, AF_0473 / 発現宿主: ![]() ![]() ![]() 参照: UniProt: O29777, ![]() |
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-実験情報
-実験
実験 | 手法: ![]() |
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EM実験 | 試料の集合状態: HELICAL ARRAY / 3次元再構成法: らせん対称体再構成法 |
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試料調製
構成要素 | 名称: deltaC-CopA in DMPC-DOPE lipids / タイプ: COMPLEX 詳細: DeltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg/mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out for 5 ...詳細: DeltaC-CopA tubular crystals were grown with a 4-to-1 mixture of DMPC-DOPE at a protein concentration of 1 mg/mL and at a lipid-to-protein weight ratio of 0.4. Dialysis was carried out for 5 days in 50 uL dialysis buttons at 303K against 500 mL of 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, and 2 mM beta-mercaptoethanol. Stock solutions of lipid were made in dodecyl octaethylene glycol ether (C12E8) at 1 mg lipid per 2 mg detergent. |
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分子量 | 値: 0.077 MDa / 実験値: NO |
緩衝液 | pH: 6.1 詳細: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, 2 mM beta-mercaptoethanol |
試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色![]() ![]() 詳細: 50 mM MES, pH 6.1, 25 mM Na2SO4, 25 mM K2SO4, 200 uM BCDS, 10 mM MgSO4, 2 mM beta-mercaptoethanol |
急速凍結![]() | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / Temp: 77 K / 手法: blot for 5 seconds before plunging |
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電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM200FEG / 日付: 2009年1月1日 |
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電子銃 | 電子線源![]() ![]() |
電子レンズ | モード: BRIGHT FIELD![]() ![]() |
試料ホルダ | 試料ホルダーモデル: GATAN LIQUID NITROGEN / 資料ホルダタイプ: CT3500 / 温度: 100 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | フィルム・検出器のモデル: KODAK SO-163 FILM |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
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解析
EMソフトウェア | 名称: EMIP / カテゴリ: 3次元再構成 | ||||||||||||
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CTF補正![]() | 詳細: each tube-crystal | ||||||||||||
3次元再構成![]() | 手法: Fourier-Bessel / 解像度: 10 Å / 解像度の算出法: OTHER / 対称性のタイプ: HELICAL | ||||||||||||
精密化ステップ | サイクル: LAST
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