+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6irh | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class III | ||||||||||||||||||
要素 |
| ||||||||||||||||||
キーワード | MEMBRANE PROTEIN / ionotropic glutamate receptors / NMDA receptors / synaptic protein | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / regulation of monoatomic cation transmembrane transport ...excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / glutamate receptor signaling pathway / NMDA glutamate receptor activity / Neurexins and neuroligins / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / glycine binding / positive regulation of calcium ion transport into cytosol / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / startle response / regulation of neuronal synaptic plasticity / monoatomic cation transmembrane transport / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / Long-term potentiation / ligand-gated monoatomic ion channel activity / excitatory synapse / neurogenesis / positive regulation of synaptic transmission, glutamatergic / calcium ion homeostasis / synaptic cleft / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / sensory perception of pain / EPHB-mediated forward signaling / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / negative regulation of protein catabolic process / long-term synaptic potentiation / postsynaptic density membrane / visual learning / cytoplasmic vesicle membrane / protein catabolic process / brain development / regulation of synaptic plasticity / terminal bouton / memory / response to wounding / synaptic vesicle / signaling receptor activity / presynaptic membrane / RAF/MAP kinase cascade / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / response to ethanol / learning or memory / dendritic spine / calmodulin binding / postsynaptic density / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / glutamatergic synapse / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.8 Å | ||||||||||||||||||
データ登録者 | Zhang, J. / Chang, S. / Zhang, X. / Zhu, S. | ||||||||||||||||||
資金援助 | 中国, 5件
| ||||||||||||||||||
引用 | ジャーナル: Cell Rep / 年: 2018 タイトル: Structural Basis of the Proton Sensitivity of Human GluN1-GluN2A NMDA Receptors. 著者: Jin-Bao Zhang / Shenghai Chang / Pan Xu / Miao Miao / Hangjun Wu / Youyi Zhang / Tongtong Zhang / Han Wang / Jilin Zhang / Chun Xie / Nan Song / Cheng Luo / Xing Zhang / Shujia Zhu / 要旨: N-methyl-D-aspartate (NMDA) receptors are critical for synaptic development and plasticity. While glutamate is the primary agonist, protons can modulate NMDA receptor activity at synapses during ...N-methyl-D-aspartate (NMDA) receptors are critical for synaptic development and plasticity. While glutamate is the primary agonist, protons can modulate NMDA receptor activity at synapses during vesicle exocytosis by mechanisms that are unknown. We used cryo-electron microscopy to solve the structures of the human GluN1-GluN2A NMDA receptor at pH 7.8 and pH 6.3. Our structures demonstrate that the proton sensor predominantly resides in the N-terminal domain (NTD) of the GluN2A subunit and reveal the allosteric coupling mechanism between the proton sensor and the channel gate. Under high-pH conditions, the GluN2A-NTD adopts an "open-and-twisted" conformation. However, upon protonation at the lower pH, the GluN2A-NTD transits from an open- to closed-cleft conformation, causing rearrangements between the tetrameric NTDs and agonist-binding domains. The conformational mobility observed in our structures (presumably from protonation) is supported by molecular dynamics simulation. Our findings reveal the structural mechanisms by which protons allosterically inhibit human GluN1-GluN2A receptor activity. | ||||||||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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 | 6irh.cif.gz | 533.9 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6irh.ent.gz | 444.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6irh.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 | 6irh_validation.pdf.gz | 828 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6irh_full_validation.pdf.gz | 971.8 KB | 表示 | |
XML形式データ | 6irh_validation.xml.gz | 103.1 KB | 表示 | |
CIF形式データ | 6irh_validation.cif.gz | 150.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ir/6irh ftp://data.pdbj.org/pub/pdb/validation_reports/ir/6irh | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
#1: タンパク質 | 分子量: 95336.219 Da / 分子数: 2 / 変異: G612R / 由来タイプ: 組換発現 / 詳細: 2 mM Glycine / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GRIN1, NMDAR1 / 細胞株 (発現宿主): HEK293S GnTl- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q05586 #2: タンパク質 | 分子量: 94192.172 Da / 分子数: 2 / 変異: E656R, E657R / 由来タイプ: 組換発現 / 詳細: 2 mM L-Glutamate / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GRIN2A, NMDAR2A / 細胞株 (発現宿主): HEK293S GnTl- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q12879 |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: Human GluN1/GluN2A NMDA receptors in the glutamate/glycine bound state at pH 6.3, Class III タイプ: COMPLEX / 詳細: with the presence of Glycine,L-glutamate and EDTA / Entity ID: all / 由来: RECOMBINANT | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 値: 0.38 MDa / 実験値: NO | |||||||||||||||||||||||||||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | |||||||||||||||||||||||||||||||||||||||||||||
由来(組換発現) | 生物種: Homo sapiens (ヒト) / 細胞: HEK293S GnTl- / プラスミド: pEG-Bacmam | |||||||||||||||||||||||||||||||||||||||||||||
緩衝液 | pH: 6.3 / 詳細: Solutions were made fresh. | |||||||||||||||||||||||||||||||||||||||||||||
緩衝液成分 |
| |||||||||||||||||||||||||||||||||||||||||||||
試料 | 濃度: 3.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: Tetrameric GluN1/GluN2A NMDA receptors | |||||||||||||||||||||||||||||||||||||||||||||
試料支持 | 詳細: 15 mA / グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 291 K / 詳細: blot for 2 seconds before plunging in liquid ethane |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 平均露光時間: 12 sec. / 電子線照射量: 56 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 4 |
画像スキャン | 動画フレーム数/画像: 40 / 利用したフレーム数/画像: 1-40 |
-解析
EMソフトウェア |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 722287 | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 7.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 86215 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||||||||||
原子モデル構築 |
|