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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: 2aix | ||||||
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タイトル | X-ray structure of the GLUR2 ligand-binding core (S1S2J) in complex with (s)-thio-atpa at 2.2 a resolution. | ||||||
![]() | Glutamate receptor 2 | ||||||
![]() | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR GLUR2 / LIGAND-BINDING CORE / AGONIST 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 | ![]() ![]() ![]() | ||||||
![]() | Kastrup, J.S. | ||||||
![]() | ![]() タイトル: Distinct kinetics of ionotropic glutamate receptor 2 splice variants characterized by fast agonist application and crystallization of a receptor-ligand complex. 著者: Holm, M.M. / Lunn, M.L. / Traynelis, S.F. / Kastrup, J.S. / Egebjerg, J. #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: Mechanisms 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: Mechanism of Glutamate Receptor Desensitization. 著者: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. #4: ![]() 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 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE RECEPTOR CONSISTS OF FOUR SUBUNITS CONSTITUTING A TETRAMER. ONE DIMER OF THE TETRAMER CAN BE GENERATED IN THE CRYSTAL. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). | ||||||
Remark 999 | SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand- ...SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand-binding core of GluR2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residues 115-116). Therefore, the sequence matches discontinuously with the reference database (413-527, 653-796). |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 71.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 50.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 446.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 450.4 KB | 表示 | |
XML形式データ | ![]() | 14.6 KB | 表示 | |
CIF形式データ | ![]() | 21.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1m5bS S: 精密化の開始モデル |
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類似構造データ |
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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: 29221.682 Da / 分子数: 1 / 断片: GLUR2-FLOP LIGAND-BINDING CORE (S1S2J). / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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#2: 化合物 | ChemComp-U1K / ( |
#3: 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: 2.42 Å3/Da / 溶媒含有率: 48.8 % |
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結晶化 | 温度: 279 K / pH: 6.5 詳細: SODIUM CHLORIDE, CACODYLATE, PEG 8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2000年10月14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: 1.0835 Å / 相対比: 1 |
反射 | 解像度: 2.17→20 Å / Num. obs: 15624 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / 冗長度: 6.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.6 |
反射 シェル | 解像度: 2.17→2.25 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 7.6 / % possible all: 93.4 |
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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: PDB ENTRY 1M5B. 解像度: 2.17→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1987987.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED. / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: ENGH & HUBER 詳細: THE FIRST THREE N-TERMINAL RESIDUES AND THE LAST TWO C-TERMINAL RESIDUES WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 60.3512 Å2 / ksol: 0.414103 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 25.7 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.17→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.17→2.31 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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