+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1m5b | ||||||
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タイトル | X-RAY STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) IN COMPLEX WITH 2-Me-Tet-AMPA AT 1.85 A RESOLUTION. | ||||||
要素 | Glutamate receptor 2GRIA2 | ||||||
キーワード | MEMBRANE PROTEIN (膜タンパク質) / Ionotropic glutamate receptor / GluR2 (GRIA2) / ligand binding core / agonist complex (アゴニスト) | ||||||
機能・相同性 | 機能・相同性情報 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 / presynaptic active zone membrane / glutamate-gated receptor activity / 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 / ionotropic glutamate receptor binding / 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 / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / シナプス小胞 / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / 成長円錐 / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / 樹状突起スパイン / postsynaptic density / neuron projection / 神経繊維 / neuronal cell body / glutamatergic synapse / シナプス / 樹状突起 / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / 細胞膜 / 小胞体 / protein-containing complex / 生体膜 / identical protein binding / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||
手法 | X線回折 / Difference Fourier. / 解像度: 1.85 Å | ||||||
データ登録者 | Hogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2002 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: ジャーナル: Neuron / 年: 2000 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: ジャーナル: Nature / 年: 2002 タイトル: Mechanism of glutamate receptor desensitization. 著者: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. #3: ジャーナル: Protein Sci. / 年: 1998 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 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. |
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1m5b.cif.gz | 185.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1m5b.ent.gz | 154 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1m5b.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/m5/1m5b ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m5b | 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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2 |
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3 |
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単位格子 |
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詳細 | The biological assembly is a dimer. Chain A and chain C of the asymmetric unit form a non-crystallographic dimer. The dimer of chain B can be generated by the two fold axis: -x, -y, z. |
-要素
#1: タンパク質 | 分子量: 29221.682 Da / 分子数: 3 / 断片: flop ligand binding core (S1S2J) / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: GluR-2 / プラスミド: pET30B / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P19491 #2: 化合物 | ChemComp-ZN / #3: 化合物 | #4: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.54 Å3/Da / 溶媒含有率: 0.515 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 6.5 詳細: PEG 8000, Zn(OAc)2, cacodylate, pH 6.5, 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: 回転陽極 / タイプ: RIGAKU / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2000年3月31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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.85→20 Å / Num. all: 76427 / Num. obs: 76427 / % possible obs: 99 % / Observed criterion σ(I): -3 / 冗長度: 6.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19 |
反射 シェル | 解像度: 1.85→1.97 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.4 / % possible all: 91.4 |
反射 | *PLUS 最低解像度: 20 Å / 冗長度: 4.4 % |
反射 シェル | *PLUS % possible obs: 91.4 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: Difference Fourier. 開始モデル: PDB entry 1FTM(S1S2J-AMPA, molecule A). 解像度: 1.85→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2171714 / Data cutoff high rms absF: 2171714 / 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 A24, GLU A122, ARG A172, LYS B183, LYS ...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 A24, GLU A122, ARG A172, LYS B183, LYS C21, MET C25, GLU C27, ARG C163, LYS C204
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 42.9979 Å2 / ksol: 0.349853 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 22.9 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: 1.85→20 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→1.97 Å / Rfactor Rfree error: 0.009 / 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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