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

Basic information

Entry

Database: EMDB / ID: EMD-64947

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

Sample

• Complex: GPCR signaling complex

• Keywords: GPCR / membrane protein / complex

Function / homology

Function:

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 / positive regulation of protein localization to cell cortex / MECP2 regulates neuronal receptors and channels / behavioral response to cocaine / T cell migration / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / axon terminus / 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 / locomotory behavior / cellular response to glucose stimulus / 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to estrogen / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / GDP binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / synaptic vesicle membrane / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / 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) / retina development in camera-type eye / cellular response to lipopolysaccharide / G protein activity / presynaptic membrane / GTPase binding / Ca2+ pathway / fibroblast proliferation / midbody

Domain/homology:

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

Component:

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

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 2.76 Å
• Authors: Suno-Ikeda C / Sugita Y / Hirose M / Suno R

Funding support

Japan, 3 items

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

• Citation: Journal: Nat Commun / Year: 2025; Title: Structural and dynamic insights into the biased signaling mechanism of the human kappa opioid receptor.; Authors: 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 / ; Abstract: 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.

History

Deposition	Jun 5, 2025	-
Header (metadata) release	Nov 19, 2025	-
Map release	Nov 19, 2025	-
Update	Nov 19, 2025	-
Current status	Nov 19, 2025	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_64947.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.675 Å

Density

Contour Level	By AUTHOR: 0.1
Minimum - Maximum	-1.2173486 - 1.6059527
Average (Standard dev.)	-0.0002330702 (±0.030321388)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 243.0 Å α=β=γ: 90.0 °

Supplemental data

Half map: #1

• File: emd_64947_half_map_1.map

Half map: #2

• File: emd_64947_half_map_2.map

Sample components

Entire : GPCR signaling complex

• Entire: Name: GPCR signaling complex

Components

• Complex: GPCR signaling complex

Supramolecule #1: GPCR signaling complex

• Supramolecule: Name: GPCR signaling complex / type: complex / ID: 1 / Parent: 0
• Source (natural): Organism: Homo sapiens (human)

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: NONE

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

6vi4

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7066947
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD