+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6b3j | |||||||||||||||
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タイトル | 3.3 angstrom phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor-Gs complex | |||||||||||||||
要素 |
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キーワード | SIGNALING PROTEIN / class B G protein-coupled receptor / agonist-receptor-G protein ternary complex / glucagon-like peptide 1 receptor / active-state G protein-coupled receptor / phase plate / phase contrast / single particle cryo-em | |||||||||||||||
機能・相同性 | 機能・相同性情報 glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / PKA activation in glucagon signalling / hair follicle placode formation ...glucagon-like peptide 1 receptor activity / glucagon receptor activity / hormone secretion / positive regulation of blood pressure / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / PKA activation in glucagon signalling / hair follicle placode formation / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / developmental growth / D1 dopamine receptor binding / intracellular transport / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / beta-2 adrenergic receptor binding / adenylate cyclase activator activity / negative regulation of blood pressure / cAMP-mediated signaling / trans-Golgi network membrane / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / G-protein beta/gamma-subunit complex binding / bone development / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / cognition / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / platelet aggregation / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / transmembrane signaling receptor activity / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / sensory perception of smell / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / positive regulation of cold-induced thermogenesis / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / learning or memory / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) Lama glama (ラマ) synthetic construct (人工物) | |||||||||||||||
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: 3.3 Å | |||||||||||||||
データ登録者 | Liang, Y.L. / Khoshouei, M. / Glukhova, A. / Furness, S.G.B. / Koole, C. / Zhao, P. / Clydesdale, L. / Thal, D.M. / Radjainia, M. / Danev, R. ...Liang, Y.L. / Khoshouei, M. / Glukhova, A. / Furness, S.G.B. / Koole, C. / Zhao, P. / Clydesdale, L. / Thal, D.M. / Radjainia, M. / Danev, R. / Baumeister, W. / Wang, M.W. / Miller, L.J. / Christopoulos, A. / Sexton, P.M. / Wootten, D. | |||||||||||||||
資金援助 | オーストラリア, 4件
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引用 | ジャーナル: Nature / 年: 2018 タイトル: Phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor-Gs complex. 著者: Yi-Lynn Liang / Maryam Khoshouei / Alisa Glukhova / Sebastian G B Furness / Peishen Zhao / Lachlan Clydesdale / Cassandra Koole / Tin T Truong / David M Thal / Saifei Lei / Mazdak Radjainia / ...著者: Yi-Lynn Liang / Maryam Khoshouei / Alisa Glukhova / Sebastian G B Furness / Peishen Zhao / Lachlan Clydesdale / Cassandra Koole / Tin T Truong / David M Thal / Saifei Lei / Mazdak Radjainia / Radostin Danev / Wolfgang Baumeister / Ming-Wei Wang / Laurence J Miller / Arthur Christopoulos / Patrick M Sexton / Denise Wootten / 要旨: The class B glucagon-like peptide-1 (GLP-1) G protein-coupled receptor is a major target for the treatment of type 2 diabetes and obesity. Endogenous and mimetic GLP-1 peptides exhibit biased agonism- ...The class B glucagon-like peptide-1 (GLP-1) G protein-coupled receptor is a major target for the treatment of type 2 diabetes and obesity. Endogenous and mimetic GLP-1 peptides exhibit biased agonism-a difference in functional selectivity-that may provide improved therapeutic outcomes. Here we describe the structure of the human GLP-1 receptor in complex with the G protein-biased peptide exendin-P5 and a Gα heterotrimer, determined at a global resolution of 3.3 Å. At the extracellular surface, the organization of extracellular loop 3 and proximal transmembrane segments differs between our exendin-P5-bound structure and previous GLP-1-bound GLP-1 receptor structure. At the intracellular face, there was a six-degree difference in the angle of the Gαs-α5 helix engagement between structures, which was propagated across the G protein heterotrimer. In addition, the structures differed in the rate and extent of conformational reorganization of the Gα protein. Our structure provides insights into the molecular basis of biased agonism. | |||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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 | 6b3j.cif.gz | 217.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6b3j.ent.gz | 171.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6b3j.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/b3/6b3j ftp://data.pdbj.org/pub/pdb/validation_reports/b3/6b3j | 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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1 |
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-要素
-Guanine nucleotide-binding protein ... , 3種, 3分子 ABG
#3: タンパク質 | 分子量: 45683.434 Da / 分子数: 1 Mutation: S54N, G226A, E268A, N271K, N274D, R280K, T284D, I285T 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GNAS, GNAS1, GSP / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P63092 |
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#4: タンパク質 | 分子量: 38534.062 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GNB1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P62873 |
#5: タンパク質 | 分子量: 7861.143 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GNG2 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P59768 |
-タンパク質 / タンパク質・ペプチド / 抗体 , 3種, 3分子 RPN
#1: タンパク質 | 分子量: 56748.418 Da / 分子数: 1 / 断片: residues 24-463 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GLP1R / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P43220 |
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#2: タンパク質・ペプチド | 分子量: 4228.670 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
#6: 抗体 | 分子量: 15140.742 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli (大腸菌) |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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: Complex of a full-length, active-state glucagon-like peptide-1 receptor with exendin-P5 ligand, heterotrimeric Gs protein and nanobody 35. タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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分子量 | 値: 0.15 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: Trichoplusia ni (イラクサキンウワバ) |
緩衝液 | pH: 7.5 |
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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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: OTHER |
電子レンズ | モード: BRIGHT FIELD / 倍率(補正後): 47170 X / Cs: 2.7 mm / C2レンズ絞り径: 50 µm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 8 sec. / 電子線照射量: 50 e/Å2 / 検出モード: COUNTING 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: 1 / 実像数: 2793 |
電子光学装置 | エネルギーフィルター名称: Gatan Quantum energy filter 位相板: The images were taken at 500 defocus |
画像スキャン | 横: 3838 / 縦: 3710 / 動画フレーム数/画像: 50 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.12_2829: / 分類: 精密化 | |||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | 詳細: Phase plate CTF correction / タイプ: NONE | |||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 614883 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||
原子モデル構築 | 詳細: 3C5T was rigid body fitted with minimal manual adjustments. The rest of the chain R and chains A,B,G,N were extensively remodeled. Chain P was built de novo. | |||||||||||||||||||||||||||||||||||
原子モデル構築 |
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拘束条件 |
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