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- PDB-9zzo: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1 -

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Basic information

Entry
Database: PDB / ID: 9zzo
TitleMP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
Components
  • Fab30 heavy chain
  • Fab30 light chain
  • Isoform 1B of Beta-arrestin-1
  • Kappa-type opioid receptor,Vasopressin V2 receptor
  • Nanobody 32
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / KAPPA OPIOID Receptor / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


response to acrylamide / dynorphin receptor activity / regulation of saliva secretion / renal water retention / sensory perception of temperature stimulus / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / positive regulation of eating behavior ...response to acrylamide / dynorphin receptor activity / regulation of saliva secretion / renal water retention / sensory perception of temperature stimulus / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / positive regulation of eating behavior / renal water absorption / adenylate cyclase-inhibiting opioid receptor signaling pathway / angiotensin receptor binding / negative regulation of luteinizing hormone secretion / TGFBR3 regulates TGF-beta signaling / G protein-coupled opioid receptor activity / Activation of SMO / hemostasis / telencephalon development / G protein-coupled opioid receptor signaling pathway / negative regulation of interleukin-8 production / positive regulation of dopamine secretion / desensitization of G protein-coupled receptor signaling pathway / positive regulation of potassium ion transmembrane transport / receptor serine/threonine kinase binding / maternal behavior / arrestin family protein binding / positive regulation of p38MAPK cascade / G protein-coupled receptor internalization / : / neuropeptide binding / sensory perception / Lysosome Vesicle Biogenesis / stress fiber assembly / positive regulation of cardiac muscle hypertrophy / eating behavior / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / pseudopodium / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / positive regulation of vasoconstriction / endocytic vesicle / estrous cycle / conditioned place preference / activation of adenylate cyclase activity / cellular response to hormone stimulus / MECP2 regulates neuronal receptors and channels / insulin-like growth factor receptor binding / behavioral response to cocaine / clathrin-coated pit / response to cytokine / negative regulation of protein ubiquitination / T-tubule / sensory perception of pain / intracellular glucose homeostasis / enzyme inhibitor activity / cytoplasmic vesicle membrane / axon terminus / Peptide ligand-binding receptors / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / sarcoplasmic reticulum / response to nicotine / clathrin-coated endocytic vesicle membrane / neuropeptide signaling pathway / cellular response to glucose stimulus / locomotory behavior / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to insulin / positive regulation of protein phosphorylation / response to estrogen / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / Vasopressin regulates renal water homeostasis via Aquaporins / Cargo recognition for clathrin-mediated endocytosis / protein transport / synaptic vesicle membrane / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to lipopolysaccharide / presynaptic membrane / cytoplasmic vesicle / defense response to virus / G alpha (i) signalling events / molecular adaptor activity / G alpha (s) signalling events / ubiquitin-dependent protein catabolic process
Similarity search - Function
Kappa opioid receptor / Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain ...Kappa opioid receptor / Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Opioid receptor / Arrestin-like, C-terminal / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / Immunoglobulin E-set / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Chem-CVV / Chem-PIO / Vasopressin V2 receptor / Kappa-type opioid receptor / Beta-arrestin-1
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHan, J. / Chen, M. / Che, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143061 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural dynamics of kappa opioid receptor interactions with β-arrestin 1.
Authors: Jianming Han / Eve J Fine / Qianru Jiang / Yuxuan Zhuang / Carl-Mikael Suomivuori / Zi-Wei Chen / Elizabeth Denn / Kyle Whiddon / Kunpeng Li / Alex S Evers / James Fuller / Joshua Carter / ...Authors: Jianming Han / Eve J Fine / Qianru Jiang / Yuxuan Zhuang / Carl-Mikael Suomivuori / Zi-Wei Chen / Elizabeth Denn / Kyle Whiddon / Kunpeng Li / Alex S Evers / James Fuller / Joshua Carter / Jonathan F Fay / Muyuan Chen / Ron O Dror / Tao Che /
Abstract: Opioid receptors signal through Gi/o protein and β-arrestin pathways that mediate distinct effects of opiate drugs. While opioid binding and G protein activation are well studied, β-arrestin ...Opioid receptors signal through Gi/o protein and β-arrestin pathways that mediate distinct effects of opiate drugs. While opioid binding and G protein activation are well studied, β-arrestin recruitment remains poorly understood. Here, we determine the complex structure of the kappa opioid receptor (KOR) with β-arrestin1 (βarr1) at 2.60 Å resolution using cryogenic electron microscopy. Structural and mass spectrometry analyses reveal multiple phosphorylation sites and a phospholipid-binding site that specifically enhances arrestin recruitment. The KOR-βarr1 complex adopts a core interaction and exhibits notable differences from other GPCR-βarr1 complexes. Comparisons with the structures of KOR-Nb39 and KOR-Gi1 complexes also reveal distinct structural features in the orthosteric binding site and the KOR-transducer interface that affect signaling bias. Using extensive 3D variation analysis and molecular dynamics simulations, we identify a range of conformational dynamics in both the receptor and βarr1, suggesting an allosteric pathway for arrestin's entry and exit.
History
DepositionJan 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Nanobody 32
C: Isoform 1B of Beta-arrestin-1
A: Kappa-type opioid receptor,Vasopressin V2 receptor
H: Fab30 heavy chain
L: Fab30 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2377
Polymers144,9365
Non-polymers1,3012
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules CA

#2: Protein Isoform 1B of Beta-arrestin-1 / Arrestin beta-1 / Non-visual arrestin-2


Mass: 43358.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB1, ARR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49407
#3: Protein Kappa-type opioid receptor,Vasopressin V2 receptor / K-OR-1 / KOR-1 / V2R / AVPR V2 / Antidiuretic hormone receptor / Renal-type arginine vasopressin receptor


Mass: 38723.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPRK1, OPRK, AVPR2, ADHR, DIR, DIR3, V2R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41145, UniProt: P30518

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Antibody , 3 types, 3 molecules EHL

#1: Antibody Nanobody 32


Mass: 13665.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)
#4: Antibody Fab30 heavy chain


Mass: 25754.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#5: Antibody Fab30 light chain


Mass: 23435.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3
#7: Chemical ChemComp-CVV / N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide


Mass: 554.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27IN2O3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 16000

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2SerialEMimage acquisition
13EMAN23D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163293 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038828
ELECTRON MICROSCOPYf_angle_d0.81212069
ELECTRON MICROSCOPYf_dihedral_angle_d5.8111279
ELECTRON MICROSCOPYf_chiral_restr0.0481441
ELECTRON MICROSCOPYf_plane_restr0.0051499

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