+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5k47 | |||||||||
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タイトル | CryoEM structure of the human Polycystin-2/PKD2 TRP channel | |||||||||
要素 | Polycystin-2 | |||||||||
キーワード | TRANSPORT PROTEIN / ion channel / transient receptor potential channel / polycystic kidney disease / Structural Genomics / Structural Genomics Consortium / SGC | |||||||||
機能・相同性 | 機能・相同性情報 detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / basal cortex / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / cation channel complex / calcium-induced calcium release activity / muscle alpha-actinin binding / voltage-gated monoatomic ion channel activity / regulation of calcium ion import / placenta blood vessel development / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / cellular response to fluid shear stress / non-motile cilium / cellular response to osmotic stress / actinin binding / voltage-gated monoatomic cation channel activity / motile cilium / aorta development / transcription regulator inhibitor activity / determination of left/right symmetry / inorganic cation transmembrane transport / neural tube development / voltage-gated sodium channel activity / ciliary membrane / protein heterotetramerization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / negative regulation of ryanodine-sensitive calcium-release channel activity / cytoplasmic side of endoplasmic reticulum membrane / centrosome duplication / cell surface receptor signaling pathway via JAK-STAT / voltage-gated potassium channel activity / potassium channel activity / embryonic placenta development / voltage-gated calcium channel activity / sodium ion transmembrane transport / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to cAMP / potassium ion transmembrane transport / cytoskeletal protein binding / cellular response to calcium ion / liver development / basal plasma membrane / ciliary basal body / establishment of localization in cell / calcium ion transmembrane transport / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / protein tetramerization / cytoplasmic vesicle membrane / cilium / mitotic spindle / Wnt signaling pathway / intracellular calcium ion homeostasis / cellular response to reactive oxygen species / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / heart development / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / ATPase binding / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / cell surface receptor signaling pathway / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
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: 4.22 Å | |||||||||
データ登録者 | Pike, A.C.W. / Grieben, M. / Shintre, C.A. / Tessitore, A. / Shrestha, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Burgess-Brown, N.A. / Huiskonen, J.T. ...Pike, A.C.W. / Grieben, M. / Shintre, C.A. / Tessitore, A. / Shrestha, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2017 タイトル: Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2). 著者: Mariana Grieben / Ashley C W Pike / Chitra A Shintre / Elisa Venturi / Sam El-Ajouz / Annamaria Tessitore / Leela Shrestha / Shubhashish Mukhopadhyay / Pravin Mahajan / Rod Chalk / Nicola A ...著者: Mariana Grieben / Ashley C W Pike / Chitra A Shintre / Elisa Venturi / Sam El-Ajouz / Annamaria Tessitore / Leela Shrestha / Shubhashish Mukhopadhyay / Pravin Mahajan / Rod Chalk / Nicola A Burgess-Brown / Rebecca Sitsapesan / Juha T Huiskonen / Elisabeth P Carpenter / 要旨: Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the ...Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the structure of human PC2 in a closed conformation, solved by electron cryomicroscopy at 4.2-Å resolution. The structure reveals a novel polycystin-specific 'tetragonal opening for polycystins' (TOP) domain tightly bound to the top of a classic transient receptor potential (TRP) channel structure. The TOP domain is formed from two extensions to the voltage-sensor-like domain (VSLD); it covers the channel's endoplasmic reticulum lumen or extracellular surface and encloses an upper vestibule, above the pore filter, without blocking the ion-conduction pathway. The TOP-domain fold is conserved among the polycystins, including the homologous channel-like region of PC1, and is the site of a cluster of ADPKD-associated missense variants. Extensive contacts among the TOP-domain subunits, the pore and the VSLD provide ample scope for regulation through physical and chemical stimuli. | |||||||||
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 | 5k47.cif.gz | 392.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5k47.ent.gz | 324.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5k47.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 | 5k47_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5k47_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 5k47_validation.xml.gz | 56.5 KB | 表示 | |
CIF形式データ | 5k47_validation.cif.gz | 86.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/k4/5k47 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/5k47 | 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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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域:
NCSアンサンブル:
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-要素
#1: タンパク質 | 分子量: 63986.668 Da / 分子数: 4 / 断片: UNP residues 185-723 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PKD2, TRPP2 / プラスミド: pFB-CT10HF-LIC 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q13563 #2: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: 糖 | ChemComp-NAG / |
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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 | 名称: Polycystin-2 channel tetramer (residues 185-723) / タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / 由来: RECOMBINANT | |||||||||||||||||||||||||
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分子量 | 値: 0.256 MDa / 実験値: NO | |||||||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | |||||||||||||||||||||||||
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) プラスミド: pFB-CT10HF-LIC | |||||||||||||||||||||||||
緩衝液 | pH: 7.5 | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 4.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Sample was monodisperse after size exclusion chromatography | |||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: C-flat | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 90 % / 凍結前の試料温度: 85 K 詳細: 3 microlitres were applied to the grid and blotted for 3secs prior to plunge in liquid ethane |
-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 |
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): 37037 X / 最大 デフォーカス(公称値): 4500 nm / 最小 デフォーカス(公称値): 1100 nm / Cs: 2 mm |
試料ホルダ | 凍結剤: NITROGEN / 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC |
撮影 | 平均露光時間: 8.8 sec. / 電子線照射量: 45.1 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 1 / 実像数: 758 詳細: Images were collected in movie-mode at 2.5 frames per second for a duration of 8.8secs |
電子光学装置 | エネルギーフィルター名称: GIF Quantum / エネルギーフィルター 上限: 20 eV / エネルギーフィルター 下限: 0 eV |
画像スキャン | 動画フレーム数/画像: 22 / 利用したフレーム数/画像: 1-22 |
-解析
ソフトウェア | 名称: REFMAC / バージョン: 5.8.0135 / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | 詳細: CTF correction as implemented in CTTFIND4/RELION / タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 161965 詳細: Particles were autopicked using CTF-corrected template based picking algorithm in RELION using selected 2D class averages based on manually picked particles. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.22 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 19546 詳細: Resolution determined by gold-standard FSC procedure as implemented in RELION クラス平均像の数: 1 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL / 空間: RECIPROCAL / 詳細: Model was built directly into map de novo | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | 解像度: 4.2→108 Å / Cor.coef. Fo:Fc: 0.863 / SU B: 52.839 / SU ML: 0.629 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 118.923 Å2
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精密化ステップ | サイクル: 1 / 合計: 15680 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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