+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3biw | |||||||||
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タイトル | Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex | |||||||||
要素 |
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キーワード | Cell adhesion/Cell adhesion / protein-protein complex / esterase domain (エステラーゼ) / LNS domain / alpha-beta hydrolase / Cell adhesion (細胞接着) / Cell junction (細胞結合) / Glycoprotein (糖タンパク質) / Membrane (生体膜) / Postsynaptic cell membrane / Synapse (シナプス) / Transmembrane (膜貫通型タンパク質) / Alternative promoter usage / Cell adhesion-Cell adhesion COMPLEX | |||||||||
機能・相同性 | 機能・相同性情報 trans-synaptic signaling by endocannabinoid / neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / : / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness ...trans-synaptic signaling by endocannabinoid / neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / : / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / retrograde trans-synaptic signaling by trans-synaptic protein complex / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / type 1 fibroblast growth factor receptor binding / terminal button organization / neuron to neuron synapse / positive regulation of synaptic vesicle exocytosis / : / neuroligin clustering involved in postsynaptic membrane assembly / excitatory synapse assembly / postsynaptic density protein 95 clustering / cerebellar granule cell differentiation / postsynaptic specialization assembly / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / neuronal ion channel clustering / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / synapse maturation / negative regulation of filopodium assembly / maintenance of synapse structure / Neurexins and neuroligins / vocal learning / synaptic vesicle targeting / positive regulation of synapse maturation / neuroligin family protein binding / positive regulation of fibroblast growth factor receptor signaling pathway / synaptic membrane adhesion / synaptic vesicle clustering / regulation of postsynaptic density assembly / inhibitory synapse / receptor localization to synapse / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / regulation of grooming behavior / presynapse assembly / filopodium tip / regulation of synaptic vesicle cycle / protein localization to synapse / NMDA glutamate receptor clustering / neuron projection arborization / vocalization behavior / positive regulation of synaptic vesicle endocytosis / regulation of insulin secretion involved in cellular response to glucose stimulus / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / vesicle docking involved in exocytosis / neurotransmitter secretion / regulation of AMPA receptor activity / AMPA glutamate receptor clustering / filopodium assembly / neuron maturation / postsynaptic specialization membrane / acetylcholine receptor binding / positive regulation of synapse assembly / positive regulation of ruffle assembly / positive regulation of protein kinase C activity / positive regulation of filopodium assembly / positive regulation of protein localization to synapse / positive regulation of intracellular signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / synaptic vesicle transport / regulation of neuron differentiation / adult behavior / positive regulation of dendritic spine development / positive regulation of protein kinase A signaling / regulation of NMDA receptor activity / social behavior / calcium channel regulator activity / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / regulation of presynapse assembly / excitatory synapse / synaptic vesicle endocytosis / endocytic vesicle / protein targeting / GABA-ergic synapse / prepulse inhibition / axonal growth cone / synaptic cleft / presynaptic active zone membrane / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis 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: 3.5 Å | |||||||||
データ登録者 | Arac, D. / Boucard, A.A. / Ozkan, E. / Strop, P. / Newell, E. / Sudhof, T.C. / Brunger, A.T. | |||||||||
引用 | ジャーナル: Neuron / 年: 2007 タイトル: Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1beta Complex Reveal Specific Protein-Protein and Protein-Ca(2+) Interactions. 著者: Arac, D. / Boucard, A.A. / Ozkan, E. / Strop, P. / Newell, E. / Sudhof, T.C. / Brunger, A.T. | |||||||||
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 | 3biw.cif.gz | 541.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3biw.ent.gz | 446.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3biw.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/bi/3biw ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3biw | 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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単位格子 |
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非結晶学的対称性 (NCS) | NCSドメイン:
NCSアンサンブル:
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詳細 | The biological assembly is a heterotetramer of two Neurexin-1beta molecules bound to a Neuroligin-1 dimer. |
-要素
#1: タンパク質 | 分子量: 64228.961 Da / 分子数: 4 / 断片: extracellular esterase domain of Neuroligin-1 / 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: Nlgn1 / プラスミド: pAcGP67A / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q62765 #2: タンパク質 | 分子量: 26030.043 Da / 分子数: 4 / 断片: extracellular LNS domain of Neurexin-1beta / 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: Nrxn1 / プラスミド: pAcGP67A / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q63373, UniProt: Q63372*PLUS #3: 多糖 | #4: 糖 | ChemComp-NAG / #5: 化合物 | ChemComp-CA / |
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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: 2.93 Å3/Da / 溶媒含有率: 57.98 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6 詳細: 8% PEG6000, 0.1 M MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-データ収集
回折 | 平均測定温度: 130 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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放射光源 | 由来: シンクロトロン / サイト: ALS / ビームライン: 8.2.2 / 波長: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2007年9月15日 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 | モノクロメーター: Double crystal, Si(111) / 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 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 3.41→50 Å / Num. obs: 53484 / % possible obs: 92.5 % / 冗長度: 3 % / Rmerge(I) obs: 0.093 / Χ2: 1.042 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
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-位相決定
位相決定 | 手法: 分子置換 | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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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 / 解像度: 3.5→45.9 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.785 / Data cutoff high absF: 3736422 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 詳細: BULK SOLVENT MODEL USED
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 67.015 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 133.3 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: 3.5→45.9 Å
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拘束条件 |
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Refine LS restraints NCS |
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LS精密化 シェル | 解像度: 3.5→3.72 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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