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基本情報
登録情報 | データベース: PDB / ID: 1m5c | ||||||
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タイトル | X-RAY STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) IN COMPLEX WITH Br-HIBO AT 1.65 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 | ![]() ![]() ![]() | ||||||
![]() | Hogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E. | ||||||
![]() | ![]() 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.K. / Gouaux, E. #1: ![]() 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. #2: ![]() タイトル: Mechanism of glutamate receptor desensitization. 著者: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / 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, Y. / Jin, R. / Gouaux, E. | ||||||
履歴 |
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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 domain of GluR2. Transmembrane regions were genetically removed and replaced with a GLY-THR linker (residues 118 and 119). Therefore, the sequence matches discontinuously with the reference database (413-527, 653-796). Residues GLY1 and ALA2 are cloning artifacts. |
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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 | ![]() | 71.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 55.3 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 755.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 756.6 KB | 表示 | |
XML形式データ | ![]() | 15.9 KB | 表示 | |
CIF形式データ | ![]() | 24.8 KB | 表示 | |
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-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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単位格子 |
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Components on special symmetry positions |
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詳細 | The biological assembly is a dimer. The dimer of chain A can be generated by the two fold axis: -x, -y, z. |
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要素
#1: タンパク質 | 分子量: 29221.682 Da / 分子数: 1 / 断片: 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-BRH / ( |
#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: 2.31 Å3/Da / 溶媒含有率: 46.79 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 279 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5 詳細: PEG 1450, Li2SO4, phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: 2000年4月27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: 0.886 Å / 相対比: 1 |
反射 | 解像度: 1.65→20 Å / Num. all: 35035 / Num. obs: 35035 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / 冗長度: 4.2 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.7 |
反射 シェル | 解像度: 1.65→1.68 Å / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1663 / % possible all: 95.1 |
反射 | *PLUS 最低解像度: 20 Å |
反射 シェル | *PLUS % possible obs: 95.1 % |
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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 (S1S2J:2-Me-Tet-AMPA, molecule A). 解像度: 1.65→19.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1082704 / Data cutoff high rms absF: 1082704 / 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: Residues 1-3 and 262-263 were not located in the electron density map. The side chains of the following residues are not fully defined: LYS A21, GLU A30, LYS A50, LYS A69, LYS A151
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 36.9599 Å2 / ksol: 0.342057 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 21.2 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: 1.65→19.5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.65→1.75 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最低解像度: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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