+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2xky | ||||||
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タイトル | Single particle analysis of Kir2.1NC_4 in negative stain | ||||||
要素 | INWARD RECTIFIER POTASSIUM CHANNEL 2 | ||||||
キーワード | METAL TRANSPORT / ION CHANNEL / MEMBRANE PROTEIN | ||||||
機能・相同性 | 機能・相同性情報 Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / cardiac muscle cell action potential / magnesium ion transport / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / regulation of membrane repolarization ...Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / cardiac muscle cell action potential / magnesium ion transport / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / regulation of membrane repolarization / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / cardiac muscle cell action potential involved in contraction / regulation of cardiac muscle cell contraction / relaxation of cardiac muscle / regulation of monoatomic ion transmembrane transport / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / intercalated disc / voltage-gated potassium channel complex / T-tubule / phosphatidylinositol-4,5-bisphosphate binding / potassium ion transport / cellular response to mechanical stimulus / postsynaptic membrane / protein homotetramerization / dendritic spine / neuronal cell body / glutamatergic synapse / dendrite / identical protein binding / membrane / plasma membrane 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 / 溶液散乱 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 17.2 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN I, J, K, L | ||||||
データ登録者 | Fomina, S. / Howard, T.D. / Sleator, O.K. / Golovanova, M. / O'Ryan, L. / Leyland, M.L. / Grossmann, J.G. / Collins, R.F. / Prince, S.M. | ||||||
引用 | ジャーナル: Biochim Biophys Acta / 年: 2011 タイトル: Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95. 著者: Svetlana Fomina / Tina D Howard / Olivia K Sleator / Marina Golovanova / Liam O'Ryan / Mark L Leyland / J Günter Grossmann / Richard F Collins / Stephen M Prince / 要旨: The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using ...The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using Transmission Electron Microscopy in negative stain. Three types of complexes were observed in electron micrographs corresponding to a 1:1 complex, a large self-enclosed tetrad complex and extended chains of linked channel domains. Using models derived from small angle X-ray scattering experiments in which high resolution structures from X-ray crystallographic and Nuclear Magnetic Resonance studies are positioned, the envelopes from single particle analysis can be resolved as a Kir2.1NC(4):PSD-95 complex and a tetrad of this unit (Kir2.1NC(4):PSD-95)(4). The tetrad complex shows the close association of the Kir2.1 cytoplasmic domains and the influence of PSD-95 mediated self-assembly on the clustering of these channels. #1: ジャーナル: Nat Neurosci / 年: 2005 タイトル: Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification. 著者: Scott Pegan / Christine Arrabit / Wei Zhou / Witek Kwiatkowski / Anthony Collins / Paul A Slesinger / Senyon Choe / 要旨: N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. ...N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. Two new crystal structures of the cytoplasmic domains of Kir2.1 (Kir2.1(L)) and the G protein-sensitive Kir3.1 (Kir3.1(S)) channels in the absence of PIP(2) show the cytoplasmic ion-permeation pathways occluded by four cytoplasmic loops that form a girdle around the central pore (G-loop). Significant flexibility of the pore-facing G-loop of Kir2.1(L) and Kir3.1(S) suggests a possible role as a diffusion barrier between cytoplasmic and transmembrane pores. Consistent with this, mutations of the G-loop disrupted gating or inward rectification. Structural comparison shows a di-aspartate cluster on the distal end of the cytoplasmic pore of Kir2.1(L) that is important for modulating inward rectification. Taken together, these results suggest the cytoplasmic domains of Kir channels undergo structural changes to modulate gating and inward rectification. | ||||||
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 | 2xky.cif.gz | 45.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2xky.ent.gz | 26.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2xky.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 | 2xky_validation.pdf.gz | 689.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2xky_full_validation.pdf.gz | 688.8 KB | 表示 | |
XML形式データ | 2xky_validation.xml.gz | 19.7 KB | 表示 | |
CIF形式データ | 2xky_validation.cif.gz | 29 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xky ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xky | 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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1 |
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非結晶学的対称性 (NCS) | NCS oper:
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-要素
#1: タンパク質 | 分子量: 34980.273 Da / 分子数: 4 / 断片: KIR2.1 CYTOPLASMIC DOMAIN, RESIDUES 1-67,189-428 / 由来タイプ: 組換発現 / 詳細: HOMOTETRAMER OF FUSED N, C TERMINI / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / プラスミド: PET15B / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P35561 |
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-実験情報
-実験
実験 |
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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 KIR2.1, CYTOPLASMIC DOMAIN / タイプ: COMPLEX |
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緩衝液 | 名称: 20MM TRIS/HCL, 150MM NACL, 1MM REDUCED GSH, 1MM EDTA, 50MM L-GLUTAMIC ACID, 50MM L-ARGININE pH: 7.5 詳細: 20MM TRIS/HCL, 150MM NACL, 1MM REDUCED GSH, 1MM EDTA, 50MM L-GLUTAMIC ACID, 50MM L-ARGININE |
試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO |
染色 | タイプ: NEGATIVE / 染色剤: Uranyl Acetate |
試料支持 | 詳細: CARBON |
-データ収集
顕微鏡 | モデル: FEI TECNAI 10 / 詳細: LOW DOSE | |||||||||||||||||||||||||||||||||||||||
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電子銃 | 電子線源: TUNGSTEN HAIRPIN / 加速電圧: 100 kV / 照射モード: FLOOD BEAM | |||||||||||||||||||||||||||||||||||||||
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1250 nm / 最小 デフォーカス(公称値): 600 nm / Cs: 2 mm | |||||||||||||||||||||||||||||||||||||||
試料ホルダ | 傾斜角・最大: 0.1 ° / 傾斜角・最小: 0 ° | |||||||||||||||||||||||||||||||||||||||
撮影 | フィルム・検出器のモデル: GENERIC GATAN | |||||||||||||||||||||||||||||||||||||||
画像スキャン | デジタル画像の数: 22 | |||||||||||||||||||||||||||||||||||||||
放射波長 | 相対比: 1 | |||||||||||||||||||||||||||||||||||||||
Soln scatter |
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-解析
EMソフトウェア |
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CTF補正 | 詳細: PARAMETERS DETERMINED USING SCATTERING CURVE | ||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | ||||||||||||
3次元再構成 | 解像度: 17.2 Å / 粒子像の数: 49012 / ピクセルサイズ(公称値): 2.93 Å / ピクセルサイズ(実測値): 2.93 Å 詳細: THE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELATIVE TO ONE ANOTHER USING A SAXS CURVE, ...詳細: THE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELATIVE TO ONE ANOTHER USING A SAXS CURVE, THIS COMPOSITE STRUCTURE IS THEN FITTED INTO AN EM MAP. MODEL GENERATED FROM SAXS REFINEMENT USING BUNCH. PETOUKHOV, M. V. AND SVERGUN, D. I. (2005). BIOPHYS J 89, 1237-50. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1764. (DEPOSITION ID: 7401). 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL 詳細: METHOD--A MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE EXPERIMENTAL MAP BY MAXIMIZING THE CROSS- ...詳細: METHOD--A MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE EXPERIMENTAL MAP BY MAXIMIZING THE CROSS-CORRELATION WITH THE EXPERIMENTAL MAP. THE COORDINATES WERE THEN REPLACED IN THE CALCULATED MAP TO GENERATE THE FINAL ENTRY. REFINEMENT PROTOCOL--DOCKED USING CHIMERA | ||||||||||||
原子モデル構築 | PDB-ID: 1U4F Accession code: 1U4F / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化 | 最高解像度: 17.2 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 17.2 Å
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Soln scatter model | 手法: RIGID BODY MODELLING コンフォーマー選択の基準: CONFORMERS WERE CONSISTENT, BEST AGREEMENT WITH EXPERIMENTAL DATA DEPOSITED (CHI=2.6). 詳細: NUMBER OF TIME FRAMES USED 25(60S, 4.25M CAMERA), 35(60S, 1M CAMERA). PROTEIN CONCENTRATION 0.5 MG/ML (4.25M CAMERA), 4.8 MG/ML (1M CAMERA) Entry fitting list: PROGRAM PRE-BUNCH, 1U4F, C_4 SYMMETRY + SEQUENCE DATA Num. of conformers calculated: 20 / Num. of conformers submitted: 1 / Software author list: PETOUKHOV, M. V. & SVERGUN, D. I. / Software list: SASREF7/BUNCH8 |