+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4pe5 | |||||||||||||||
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タイトル | Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel | |||||||||||||||
要素 | (Glutamate receptor ionotropic, NMDA ...) x 2 | |||||||||||||||
キーワード | TRANSPORT PROTEIN / NMDA receptor / GluN1 / GluN2B / ion channel | |||||||||||||||
機能・相同性 | 機能・相同性情報 neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration ...neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / response to hydrogen sulfide / Assembly and cell surface presentation of NMDA receptors / olfactory learning / regulation of protein kinase A signaling / conditioned taste aversion / dendritic branch / response to other organism / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / positive regulation of inhibitory postsynaptic potential / apical dendrite / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / fear response / response to methylmercury / positive regulation of cysteine-type endopeptidase activity / voltage-gated monoatomic cation channel activity / cellular response to dsRNA / response to carbohydrate / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / interleukin-1 receptor binding / cellular response to lipid / NMDA glutamate receptor activity / response to morphine / positive regulation of glutamate secretion / response to growth hormone / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / response to manganese ion / NMDA selective glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of axonogenesis / regulation of dendrite morphogenesis / male mating behavior / heterocyclic compound binding / suckling behavior / receptor clustering / startle response / behavioral response to pain / response to amine / small molecule binding / regulation of neuronal synaptic plasticity / action potential / monoatomic cation transmembrane transport / monoatomic cation transport / associative learning / positive regulation of excitatory postsynaptic potential / regulation of MAPK cascade / response to magnesium ion / social behavior / ligand-gated monoatomic ion channel activity / cellular response to organic cyclic compound / excitatory synapse / extracellularly glutamate-gated ion channel activity / cellular response to glycine / positive regulation of dendritic spine maintenance / behavioral fear response / neuron development / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / postsynaptic density, intracellular component / cellular response to manganese ion / glutamate receptor binding / D2 dopamine receptor binding / multicellular organismal response to stress / long-term memory / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / monoatomic cation channel activity / detection of mechanical stimulus involved in sensory perception of pain / calcium ion homeostasis / regulation of neuron apoptotic process / synaptic cleft / response to electrical stimulus / response to mechanical stimulus / glutamate-gated receptor activity 類似検索 - 分子機能 | |||||||||||||||
生物種 | Rattus norvegicus (ドブネズミ) | |||||||||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.96 Å | |||||||||||||||
データ登録者 | Karakas, E. / Furukawa, H. | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Science / 年: 2014 タイトル: Crystal structure of a heterotetrameric NMDA receptor ion channel. 著者: Karakas, E. / Furukawa, H. | |||||||||||||||
履歴 |
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-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 | 4pe5.cif.gz | 564.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4pe5.ent.gz | 427.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4pe5.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 | 4pe5_validation.pdf.gz | 2.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4pe5_full_validation.pdf.gz | 2.1 MB | 表示 | |
XML形式データ | 4pe5_validation.xml.gz | 58.1 KB | 表示 | |
CIF形式データ | 4pe5_validation.cif.gz | 85.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pe/4pe5 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pe5 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
-Glutamate receptor ionotropic, NMDA ... , 2種, 4分子 ACBD
#1: タンパク質 | 分子量: 92680.945 Da / 分子数: 2 / 断片: UNP residues 23-847 変異: N61Q, N239D, N350Q, N471Q, N491Q, T561C, E594Q, E595S, E597S, E598T, N771Q, F810C, R844N, R845G, K846A 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: Grin1, Nmdar1 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P35439 #2: タンパク質 | 分子量: 92163.352 Da / 分子数: 2 / 断片: UNP residues 27-852 変異: S214C, N348D, D557C, C588S, I815C, C838S, C849S, del(C395), del(P396), del(E397), del(E399), del(E400), del(E402) 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: Grin2b 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q00960 |
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-糖 , 5種, 14分子
#3: 多糖 | #4: 多糖 | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #5: 多糖 | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #9: 糖 | ChemComp-NAG / |
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-非ポリマー , 4種, 90分子
#7: 化合物 | ChemComp-W / #8: 化合物 | #10: 化合物 | #11: 化合物 | |
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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: 4.2 Å3/Da / 溶媒含有率: 70.69 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.8 詳細: PEG 4000, Tris-HCl, NaCl, Magnesium acetate, metatungstate PH範囲: 8.0-8.8 |
-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: シンクロトロン / サイト: APS / ビームライン: 23-ID-B / 波長: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2013年12月7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: 1.0332 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 3.95→50 Å / Num. obs: 52241 / % possible obs: 98.6 % / 冗長度: 3.8 % / Biso Wilson estimate: 196.24 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.348 / Net I/av σ(I): 13.025 / Net I/σ(I): 9.3 / Num. measured all: 197482 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1 / Rejects: _
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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: 分子置換 開始モデル: PDB ENTRIES 3QEL, 2A5T 解像度: 3.96→29.717 Å / SU ML: 0.61 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 32.13 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 3.96→29.717 Å
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拘束条件 |
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LS精密化 シェル |
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