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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1xhy | ||||||
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タイトル | X-ray structure of the Y702F mutant of the GluR2 ligand-binding core (S1S2J) in complex with kainate at 1.85 A resolution | ||||||
![]() | Glutamate receptor | ||||||
![]() | MEMBRANE PROTEIN / Ionotropic glutamate receptor GluR2 / mutant / ligand-binding core / kainate complex | ||||||
機能・相同性 | ![]() spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Frandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Gajhede, M. / Schousboe, A. / Kastrup, J.S. | ||||||
![]() | ![]() タイトル: Tyr702 Is an Important Determinant of Agonist Binding and Domain Closure of the Ligand-Binding Core of GluR2. 著者: Frandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Fattorusso, C. / Gajhede, M. / Schousboe, A. / Kastrup, J.S. #1: ![]() タイトル: Structural basis for AMPA receptor activation and ligand selectivity: Crystal structures of five agonist complexes with the GluR2 ligand binding core. 著者: Hogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I. / Gouaux, E. #2: ![]() タイトル: Mechanism for activation and antagonism of an AMPA-sensitive glutamate receptor: Crystal structures of the GluR2 ligand binding core. 著者: Armstrong, N. / Gouaux, E. #3: ![]() タイトル: Probing the ligand binding domain of the GluR2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct. 著者: Chen, G.Q. / Sun, R. / Jin, R. / Gouaux, E. | ||||||
履歴 |
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Remark 400 | COMPOUND NATIVE GLUR2 IS A MEMBRANE PROTEIN. S1S2J COMPRISES THE LIGAND BINDING CORE OF THE PROTEIN. ...COMPOUND NATIVE GLUR2 IS A MEMBRANE PROTEIN. S1S2J COMPRISES THE LIGAND BINDING CORE OF THE PROTEIN. TRANSMEMBRANE PARTS OF THE PROTEIN HAVE BEEN REPLACED BY A GLY-THR LINKER (RESIDUES 115-116). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE. | ||||||
Remark 999 | SEQUENCE Residues 528-652 in dbref have been replaced by a Gly-Thr (115-116) linker |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロード
PDBx/mmCIF形式 | ![]() | 76.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 55 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 454.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 455.8 KB | 表示 | |
XML形式データ | ![]() | 15.9 KB | 表示 | |
CIF形式データ | ![]() | 24.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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1 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 29205.682 Da / 分子数: 1 断片: GluR2 flop ligand-binding core (S1S2J), UNP residues 413-527 and 653-796 変異: Y702F / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() | ||||
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#2: 化合物 | ChemComp-SO4 / #3: 化合物 | ChemComp-KAI / | #4: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.4 Å3/Da / 溶媒含有率: 41.6 % |
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結晶化 | 温度: 280 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: PEG1000, Li2SO4, cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-データ収集
回折 | 平均測定温度: 110 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2003年11月3日 |
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 | 波長: 0.811 Å / 相対比: 1 |
反射 | 解像度: 1.85→20.4 Å / Num. all: 24433 / Num. obs: 24433 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / 冗長度: 3.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.1 |
反射 シェル | 解像度: 1.85→1.88 Å / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3 / % possible all: 96 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 1FW0 解像度: 1.85→20.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.564 / SU ML: 0.078 / Isotropic thermal model: restrained / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.127 / 立体化学のターゲット値: Engh & Huber 詳細: Residues 1-2 and 263 were not located in the electron density map
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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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 16.048 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.85→20.37 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.85→1.886 Å / Total num. of bins used: 20 /
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