EMDB-64947: Cryo-EM structure of the human kappa opioid receptor signaling co...

基本情報

登録情報

データベース: EMDB / ID: EMD-64947

• タイトル: Cryo-EM structure of the human kappa opioid receptor signaling complex bound to compound A

試料

• 複合体: GPCR signaling complex

• キーワード: GPCR / membrane protein / complex

機能・相同性

分子機能:

response to acrylamide / adenylate cyclase-inhibiting opioid receptor signaling pathway / dynorphin receptor activity / regulation of saliva secretion / negative regulation of luteinizing hormone secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / G protein-coupled opioid receptor activity / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion / sensory perception / maternal behavior / positive regulation of potassium ion transmembrane transport / receptor serine/threonine kinase binding / positive regulation of p38MAPK cascade / neuropeptide binding / eating behavior / conditioned place preference / neuropeptide signaling pathway / estrous cycle / adenylate cyclase inhibitor activity / MECP2 regulates neuronal receptors and channels / positive regulation of protein localization to cell cortex / T cell migration / Adenylate cyclase inhibitory pathway / behavioral response to cocaine / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / axon terminus / adenylate cyclase-inhibiting serotonin receptor signaling pathway / sensory perception of pain / T-tubule / cellular response to forskolin / regulation of mitotic spindle organization / Peptide ligand-binding receptors / sarcoplasmic reticulum / response to nicotine / Regulation of insulin secretion / cellular response to glucose stimulus / locomotory behavior / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to insulin / response to peptide hormone / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / response to estrogen / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / centriolar satellite / G-protein beta/gamma-subunit complex binding / 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 / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / synaptic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / cellular response to lipopolysaccharide / retina development in camera-type eye / G protein activity / presynaptic membrane / GTPase binding / Ca2+ pathway / fibroblast proliferation / midbody

ドメイン・相同性:

Kappa opioid receptor / Opioid receptor / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase

構成要素:

Kappa-type opioid receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1

• 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: 2.76 Å
• データ登録者: Suno-Ikeda C / Sugita Y / Hirose M / Suno R

資金援助

日本, 3件

Organization	Grant number	国
Japan Society for the Promotion of Science (JSPS)	19H03428	日本
Japan Society for the Promotion of Science (JSPS)	24K02231	日本
Japan Society for the Promotion of Science (JSPS)	21H05111	日本

• 引用: ジャーナル: Nat Commun / 年: 2025; タイトル: Structural and dynamic insights into the biased signaling mechanism of the human kappa opioid receptor.; 著者: Chiyo Suno-Ikeda / Ryo Nishikawa / Riko Suzuki / Shun Yokoi / Seiya Iwata / Tomoyo Takai / Takaya Ogura / Mika Hirose / Akihisa Tokuda / Risako Katamoto / Akitoshi Inoue / Eri Asai / Ryoji Kise / Yukihiko Sugita / Takayuki Kato / Hiroshi Nagase / Ayori Mitsutake / Tsuyoshi Saitoh / Kota Katayama / Asuka Inoue / Hideki Kandori / Takuya Kobayashi / Ryoji Suno / ; 要旨: The κ-opioid receptor (KOR) is a member of the G protein-coupled receptor (GPCR) family, modulating cellular responses through transducers such as G proteins and β-arrestins. G-protein-biased KOR agonists aim to retain analgesic and antipruritic actions while limiting aversion and sedation. Aiming to inform G-biased KOR agonist design, we analyze signaling-relevant residues from structural and dynamic views. Here we show, using multiple complementary methods, shared residues that determine β-arrestin recruitment by nalfurafine and U-50,488H. Cryo-electron microscopy structures of the KOR-G signaling complexes identify the ligand binding mode in the activated state. Vibrational spectroscopy reveals ligand-induced conformational changes. Cell-based mutant experiments pinpoint four amino acids (K227, C286, H291, and Y312; Ballesteros-Weinstein numbering is shown in superscript) that play crucial roles in β-arrestin recruitment. Furthermore, MD simulations revealed that the four mutants tend to adopt conformations with reduced β-arrestin recruitment activity. Our research findings provide a foundation for enhancing KOR-mediated therapeutic effects while minimizing unwanted side effects by targeting specific residues within the KOR ligand-binding pocket, including K227 and Y312, which have previously been implicated in biased signaling.

履歴

登録	2025年6月5日	-
ヘッダ(付随情報) 公開	2025年11月19日	-
マップ公開	2025年11月19日	-
更新	2025年11月19日	-
現状	2025年11月19日	処理サイト: PDBj / 状態: 公開

マップ

• ファイル: ダウンロード / ファイル: emd_64947.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• ボクセルのサイズ: X=Y=Z: 0.675 Å

密度

表面レベル	登録者による: 0.1
最小 - 最大	-1.2173486 - 1.6059527
平均 (標準偏差)	-0.0002330702 (±0.030321388)

• 対称性: 空間群: 1

詳細

EMDB XML:

マップ形状	Axis order X Y Z Origin 0 0 0 サイズ 360 360 360 Spacing 360 360 360
セル	A=B=C: 243.0 Å α=β=γ: 90.0 °

添付データ

ハーフマップ: #1

• ファイル: emd_64947_half_map_1.map

ハーフマップ: #2

• ファイル: emd_64947_half_map_2.map

試料の構成要素

全体 : GPCR signaling complex

• 全体: 名称: GPCR signaling complex

要素

• 複合体: GPCR signaling complex

超分子 #1: GPCR signaling complex

• 超分子: 名称: GPCR signaling complex / タイプ: complex / ID: 1 / 親要素: 0
• 由来(天然): 生物種: Homo sapiens (ヒト)

実験情報

構造解析

• 手法: クライオ電子顕微鏡法
• 解析: 単粒子再構成法
• 試料の集合状態: particle

試料調製

• 緩衝液: pH: 7.5
• 凍結: 凍結剤: ETHANE

電子顕微鏡法

• 顕微鏡: TFS KRIOS
• 撮影: フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 60.0 e/Ų
• 電子線: 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
• 電子光学系: 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 1.5 µm; 最小 デフォーカス（公称値）: 0.7000000000000001 µm
• 実験機器: モデル: Titan Krios / 画像提供: FEI Company

画像解析

• CTF補正: タイプ: NONE

初期モデル

モデルのタイプ: PDB ENTRY
PDBモデル - PDB ID:

6vi4

• 最終 再構成: 解像度のタイプ: BY AUTHOR / 解像度: 2.76 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 7066947
• 初期 角度割当: タイプ: MAXIMUM LIKELIHOOD
• 最終 角度割当: タイプ: MAXIMUM LIKELIHOOD