+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j8h | ||||||
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タイトル | Structure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution | ||||||
要素 |
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キーワード | TRANSPORT PROTEIN/ISOMERASE / rabbit ryanodine receptor RyR1 / high-conductance intracellular Ca2+ channels / excitation-contraction coupling / TRANSPORT PROTEIN-ISOMERASE complex | ||||||
機能・相同性 | 機能・相同性情報 cytoplasmic side of membrane / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine ...cytoplasmic side of membrane / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / identical protein binding / membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Oryctolagus cuniculus (ウサギ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | ||||||
データ登録者 | Yan, Z. / Bai, X. / Yan, C. / Wu, J. / Scheres, S.H.W. / Shi, Y. / Yan, N. | ||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution. 著者: Zhen Yan / Xiaochen Bai / Chuangye Yan / Jianping Wu / Zhangqiang Li / Tian Xie / Wei Peng / Changcheng Yin / Xueming Li / Sjors H W Scheres / Yigong Shi / Nieng Yan / 要旨: The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest ...The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5,000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryomicroscopy. Three previously uncharacterized domains, named central, handle and helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative-charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity-filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3j8h.cif.gz | 2.5 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j8h.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 3j8h.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 | 3j8h_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j8h_full_validation.pdf.gz | 1.7 MB | 表示 | |
XML形式データ | 3j8h_validation.xml.gz | 399.8 KB | 表示 | |
CIF形式データ | 3j8h_validation.cif.gz | 611 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j8h ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j8h | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 500211.562 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: P11716 #2: タンパク質 | 分子量: 11836.508 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Oryctolagus cuniculus (ウサギ) / 遺伝子: FKBP1A, FKBP1, FKBP12 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62943, peptidylprolyl isomerase #3: 化合物 | ChemComp-ZN / |
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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 |
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緩衝液 | 名称: 20 mM MOPS sodium, pH 7.4, 250 mM NaCl, 2 mM DTT, 2 mM EGTA, 0.015% Tween20, protein inhibitors pH: 7.4 詳細: 20 mM MOPS sodium, pH 7.4, 250 mM NaCl, 2 mM DTT, 2 mM EGTA, 0.015% Tween20, protein inhibitors | ||||||||||||||||
試料 | 濃度: 0.06 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||
試料支持 | 詳細: holey carbon grids (Quantifoil CuR2/2), on which a home-made continuous carbon film (estimated to be ~30 Angstrom thick) had previously been deposited | ||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: NITROGEN / 湿度: 100 % 詳細: Protein solution was applied to glow-discharged carbon coated grid and blotted for 2 seconds before plunging into liquid nitrogen (FEI VITROBOT MARK III) 手法: protein solution was applied to glow-discharged carbon coated grid and blotted for 2 seconds before plunging |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 / 日付: 2014年6月21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): 78000 X / 倍率(補正後): 104748 X / 最大 デフォーカス(公称値): 5600 nm / 最小 デフォーカス(公称値): 1900 nm / Cs: 2 mm |
試料ホルダ | 資料ホルダタイプ: GATAN LIQUID NITROGEN / 温度: 85 K / 最高温度: 90 K / 最低温度: 80 K |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
放射波長 | 相対比: 1 |
-解析
ソフトウェア | 名称: REFMAC / バージョン: 5.8.0049 2013/08/13 / 分類: 精密化 / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk 解説: (un)restrained refinement or idealisation of macromolecular structures | ||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | 詳細: Contrast transfer function parameters were estimated using CTFFIND3 | ||||||||||||||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 65872 / ピクセルサイズ(公称値): 1.34 Å / ピクセルサイズ(実測値): 1.34 Å 詳細: All two- and three-dimensional classifications and refinements were performed using RELION 1.3. The model was built manually in COOT, and was refined in real space using Phenix and in ...詳細: All two- and three-dimensional classifications and refinements were performed using RELION 1.3. The model was built manually in COOT, and was refined in real space using Phenix and in reciprocal space using Refmac. 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 詳細: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS | ||||||||||||||||||||||||
精密化ステップ | サイクル: LAST
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