+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-42023 | |||||||||||||||
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タイトル | GPR3 Orphan G-coupled Protein Receptor in complex with Dominant Negative Gs. | |||||||||||||||
マップデータ | Sharpened Consensus map. | |||||||||||||||
試料 |
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キーワード | GPR3 / orphan GPCR / GPCR / MEMBRANE PROTEIN | |||||||||||||||
機能・相同性 | 機能・相同性情報 sphingosine-1-phosphate receptor activity / regulation of meiotic nuclear division / positive regulation of cAMP-mediated signaling / regulation of metabolic process / PKA activation in glucagon signalling / hair follicle placode formation / mu-type opioid receptor binding / developmental growth / corticotropin-releasing hormone receptor 1 binding / intracellular transport ...sphingosine-1-phosphate receptor activity / regulation of meiotic nuclear division / positive regulation of cAMP-mediated signaling / regulation of metabolic process / PKA activation in glucagon signalling / hair follicle placode formation / mu-type opioid receptor binding / developmental growth / corticotropin-releasing hormone receptor 1 binding / intracellular transport / D1 dopamine receptor binding / Hedgehog 'off' state / beta-2 adrenergic receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of cytosolic calcium ion concentration / activation of adenylate cyclase activity / adenylate cyclase activator activity / trans-Golgi network membrane / G protein-coupled receptor activity / 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 activation / G protein-coupled acetylcholine receptor signaling pathway / 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 / 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 / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / positive regulation of cold-induced thermogenesis / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / 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 / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.49 Å | |||||||||||||||
データ登録者 | Russell IC / Belousoff MJ / Sexton P | |||||||||||||||
資金援助 | オーストラリア, 4件
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引用 | ジャーナル: Biochemistry / 年: 2024 タイトル: Lipid-Dependent Activation of the Orphan G Protein-Coupled Receptor, GPR3. 著者: Isabella C Russell / Xin Zhang / Fabian Bumbak / Samantha M McNeill / Tracy M Josephs / Michael G Leeming / George Christopoulos / Hariprasad Venugopal / Maria M Flocco / Patrick M Sexton / ...著者: Isabella C Russell / Xin Zhang / Fabian Bumbak / Samantha M McNeill / Tracy M Josephs / Michael G Leeming / George Christopoulos / Hariprasad Venugopal / Maria M Flocco / Patrick M Sexton / Denise Wootten / Matthew J Belousoff / 要旨: The class A orphan G protein-coupled receptor (GPCR), GPR3, has been implicated in a variety of conditions, including Alzheimer's and premature ovarian failure. GPR3 constitutively couples with Gαs, ...The class A orphan G protein-coupled receptor (GPCR), GPR3, has been implicated in a variety of conditions, including Alzheimer's and premature ovarian failure. GPR3 constitutively couples with Gαs, resulting in the production of cAMP in cells. While tool compounds and several putative endogenous ligands have emerged for the receptor, its endogenous ligand, if it exists, remains a mystery. As novel potential drug targets, the structures of orphan GPCRs have been of increasing interest, revealing distinct modes of activation, including autoactivation, presence of constitutively activating mutations, or via cryptic ligands. Here, we present a cryo-electron microscopy (cryo-EM) structure of the orphan GPCR, GPR3 in complex with DNGαs and Gβγ. The structure revealed clear density for a lipid-like ligand that bound within an extended hydrophobic groove, suggesting that the observed "constitutive activity" was likely due to activation via a lipid that may be ubiquitously present. Analysis of conformational variance within the cryo-EM data set revealed twisting motions of the GPR3 transmembrane helices that appeared coordinated with changes in the lipid-like density. We propose a mechanism for the binding of a lipid to its putative orthosteric binding pocket linked to the GPR3 dynamics. | |||||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_42023.map.gz | 59.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-42023-v30.xml emd-42023.xml | 23.9 KB 23.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_42023_fsc.xml | 9.5 KB | 表示 | FSCデータファイル |
画像 | emd_42023.png | 46 KB | ||
マスクデータ | emd_42023_msk_1.map | 64 MB | マスクマップ | |
Filedesc metadata | emd-42023.cif.gz | 7 KB | ||
その他 | emd_42023_additional_1.map.gz emd_42023_half_map_1.map.gz emd_42023_half_map_2.map.gz | 31.7 MB 59.3 MB 59.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-42023 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42023 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_42023_validation.pdf.gz | 908.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_42023_full_validation.pdf.gz | 908 KB | 表示 | |
XML形式データ | emd_42023_validation.xml.gz | 16.2 KB | 表示 | |
CIF形式データ | emd_42023_validation.cif.gz | 20.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42023 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42023 | HTTPS FTP |
-関連構造データ
関連構造データ | 8u8fMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_42023.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Sharpened Consensus map. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.86 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_42023_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unsharpened consensus map
ファイル | emd_42023_additional_1.map | ||||||||||||
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注釈 | Unsharpened consensus map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half 1
ファイル | emd_42023_half_map_1.map | ||||||||||||
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注釈 | Half 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half 2
ファイル | emd_42023_half_map_2.map | ||||||||||||
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注釈 | Half 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Active state, GPR3 complex with Dominant negative G-alphaS.
全体 | 名称: Active state, GPR3 complex with Dominant negative G-alphaS. |
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要素 |
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-超分子 #1: Active state, GPR3 complex with Dominant negative G-alphaS.
超分子 | 名称: Active state, GPR3 complex with Dominant negative G-alphaS. タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
分子 | 名称: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 45.699434 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...文字列: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQA DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGAQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ AALKLFDSIW NNKWLRDTSV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCS VDTENIRRVF NDCRDIIQRM HLRQYELL UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
-分子 #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
分子 | 名称: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 37.413863 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: QSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...文字列: QSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-分子 #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
分子 | 名称: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 6.375332 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFR UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-分子 #4: G-protein coupled receptor 3
分子 | 名称: G-protein coupled receptor 3 / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 41.788871 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: NSTMKTIIAL SYIFCLVFAD YKDDDDLEVL FQGPAMWGAG SPLAWLSAGS GNVNVSSVGP AEGPTGPAAP LPSPKAWDVV LCISGTLVS CENALVVAII VGTPAFRAPM FLLVGSLAVA DLLAGLGLVL HFAAVFCIGS AEMSLVLVGV LAMAFTASIG S LLAITVDR ...文字列: NSTMKTIIAL SYIFCLVFAD YKDDDDLEVL FQGPAMWGAG SPLAWLSAGS GNVNVSSVGP AEGPTGPAAP LPSPKAWDVV LCISGTLVS CENALVVAII VGTPAFRAPM FLLVGSLAVA DLLAGLGLVL HFAAVFCIGS AEMSLVLVGV LAMAFTASIG S LLAITVDR YLSLYNALTY YSETTVTRTY VMLALVWGGA LGLGLLPVLA WNCLDGLTTC GVVYPLSKNH LVVLAIAFFM VF GIMLQLY AQICRIVCRH AQQIALQRHL LPASHYVATR KGIATLAVVL GAFAACWLPF TVYCLLGDAH SPPLYTYLTL LPA TYNSMI NPIIYAFRNQ DVQKVLWAVC CCCSSSKIPF RSRSPSDVPA GLEVLFQGPH HHHHHHHAAA FESR UniProtKB: G-protein coupled receptor 3 |
-分子 #5: PALMITIC ACID
分子 | 名称: PALMITIC ACID / タイプ: ligand / ID: 5 / コピー数: 1 / 式: PLM |
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分子量 | 理論値: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 4.5 mg/mL | ||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 200 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 120 sec. / 前処理 - 雰囲気: AIR | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | TFS GLACIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 最大 デフォーカス(補正後): 1.0 µm / 最小 デフォーカス(補正後): 0.5 µm / 倍率(補正後): 120000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 120000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |