+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7d7f | |||||||||
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タイトル | Structure of PKD1L3-CTD/PKD2L1 in calcium-bound state | |||||||||
要素 |
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キーワード | TRANSPORT PROTEIN / Heterotetrameric TRP channel / Calcium / Primary cilia / PKD | |||||||||
機能・相同性 | 機能・相同性情報 detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / cellular response to pH / detection of mechanical stimulus / cation channel complex / muscle alpha-actinin binding / cellular response to acidic pH ...detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / cellular response to pH / detection of mechanical stimulus / cation channel complex / muscle alpha-actinin binding / cellular response to acidic pH / non-motile cilium / inorganic cation transmembrane transport / sodium channel activity / ciliary membrane / smoothened signaling pathway / monoatomic cation transport / monoatomic cation channel activity / potassium ion transmembrane transport / calcium channel complex / protein tetramerization / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / carbohydrate binding / protein homotetramerization / transmembrane transporter binding / receptor complex / calcium ion binding / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
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: 3.1 Å | |||||||||
データ登録者 | Su, Q. / Shi, Y.G. | |||||||||
資金援助 | 中国, 2件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Structural basis for Ca activation of the heteromeric PKD1L3/PKD2L1 channel. 著者: Qiang Su / Mengying Chen / Yan Wang / Bin Li / Dan Jing / Xiechao Zhan / Yong Yu / Yigong Shi / 要旨: The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization ...The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization of heterotetrametric TRP-like channels. Here we show that a truncated PKD1L3/PKD2L1 complex with the C-terminal TRP-fold fragment of PKD1L3 retains both Ca and acid-induced channel activities. Cryo-EM structures of this core heterocomplex with or without supplemented Ca were determined at resolutions of 3.1 Å and 3.4 Å, respectively. The heterotetramer, with a pseudo-symmetric TRP architecture of 1:3 stoichiometry, has an asymmetric selectivity filter (SF) guarded by Lys2069 from PKD1L3 and Asp523 from the three PKD2L1 subunits. Ca-entrance to the SF vestibule is accompanied by a swing motion of Lys2069 on PKD1L3. The S6 of PKD1L3 is pushed inward by the S4-S5 linker of the nearby PKD2L1 (PKD2L1-III), resulting in an elongated intracellular gate which seals the pore domain. Comparison of the apo and Ca-loaded complexes unveils an unprecedented Ca binding site in the extracellular cleft of the voltage-sensing domain (VSD) of PKD2L1-III, but not the other three VSDs. Structure-guided mutagenic studies support this unconventional site to be responsible for Ca-induced channel activation through an allosteric mechanism. | |||||||||
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 | 7d7f.cif.gz | 348.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7d7f.ent.gz | 287.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7d7f.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d7/7d7f ftp://data.pdbj.org/pub/pdb/validation_reports/d7/7d7f | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 69234.734 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Pkd2l1, Trpp3 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A2A259 #2: タンパク質 | | 分子量: 62541.914 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Pkd1l3, 71B10 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2EG98 #3: 糖 | ChemComp-NAG / #4: 化合物 | ChemComp-CA / 研究の焦点であるリガンドがあるか | N | |
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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: Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.5 |
試料 | 濃度: 10 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-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: 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 |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17.1_3660: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 149903 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 最高解像度: 3 Å | ||||||||||||||||||||||||
拘束条件 |
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