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- EMDB-75011: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1 -

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Entry
Database: EMDB / ID: EMD-75011
TitleMP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
Map data
Sample
  • Complex: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Isoform 1B of Beta-arrestin-1
    • Protein or peptide: Kappa-type opioid receptor,Vasopressin V2 receptor
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
  • Ligand: [(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
  • Ligand: N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide
KeywordsGPCR / 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
Vasopressin V2 receptor / Kappa-type opioid receptor / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHan J / Chen M / Che T
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75011.png

Downloads & links

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Map

FileDownload / File: emd_75011.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 224 pix.
= 278.208 Å		1.24 Å/pix.
x 224 pix.
= 278.208 Å		1.24 Å/pix.
x 224 pix.
= 278.208 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.242 Å
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Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-16.947455999999999 - 36.342019999999998
Average (Standard dev.)0.003396575 (±1.0001322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 278.208 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_75011_additional_1.map
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Half map: #2

Fileemd_75011_half_map_1.map
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Half map: #1

Fileemd_75011_half_map_2.map
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Sample components

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Entire : MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1

EntireName: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
Components
  • Complex: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Isoform 1B of Beta-arrestin-1
    • Protein or peptide: Kappa-type opioid receptor,Vasopressin V2 receptor
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
  • Ligand: [(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
  • Ligand: N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide

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Supramolecule #1: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1

SupramoleculeName: MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nanobody 32

MacromoleculeName: Nanobody 32 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.665136 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCVVSGFFFD TVTMAWYRRA PGKHRELVAS ATAGGTTTYA DSVKDRFTIS RDNAKNTVYL QMNSLKPED TAVYYCNTFV RSLSWGQGTQ VTVSSHHHHH HEPEA

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Macromolecule #2: Isoform 1B of Beta-arrestin-1

MacromoleculeName: Isoform 1B of Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.358164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSAGDKGTRV FKKASPNGKL TVYLGKRDFV DHIDLVDPVD GVVLVDPEYL KERRVYVTLT AAFRYGREDL DVLGLTFRKD LFVANVQSF PPAPEDKKPL TRLQERLIKK LGEHAYPFTF EIPPNLPSSV TLQPGPEDTG KAIGVDYEVK AFVAENLEEK I HKRNSVRL ...String:
GSAGDKGTRV FKKASPNGKL TVYLGKRDFV DHIDLVDPVD GVVLVDPEYL KERRVYVTLT AAFRYGREDL DVLGLTFRKD LFVANVQSF PPAPEDKKPL TRLQERLIKK LGEHAYPFTF EIPPNLPSSV TLQPGPEDTG KAIGVDYEVK AFVAENLEEK I HKRNSVRL VIEKVQYAPE RPGPQPTAET TRQFLMSDKP LHLEASLDKE IYYHGEPISV NVHVTNNTNK TVKKIKISVR QY ADIVLFN TAQYKVPVAM EEADDTVAPS STFSKVYTLT PFLANNREKR GLALDGKLKH EDTNLASSTL LREGANREIL GII VSYKVK VKLVVSRGGD VAVELPFTLM HPKPKEEPPH REVPENETPV DTNLIELDTN DDDAAAEDFA R

UniProtKB: Beta-arrestin-1

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Macromolecule #3: Kappa-type opioid receptor,Vasopressin V2 receptor

MacromoleculeName: Kappa-type opioid receptor,Vasopressin V2 receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.723129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ISPAIPVIIT AVYSVVFVVG LVGNSLVMFV IIRYTKMKTA TNIYIFNLAL ADALVTTTMP FQSTVYLMNS WPFGDVLCKI VLSIDYYNM FTSIFTLTMM SVDRYIAVCH PVKALDFRTP LKAKIINICI WLLSSSVGIS AIVLGGTKVR EDVDVIECSL Q FPDDDYSW ...String:
ISPAIPVIIT AVYSVVFVVG LVGNSLVMFV IIRYTKMKTA TNIYIFNLAL ADALVTTTMP FQSTVYLMNS WPFGDVLCKI VLSIDYYNM FTSIFTLTMM SVDRYIAVCH PVKALDFRTP LKAKIINICI WLLSSSVGIS AIVLGGTKVR EDVDVIECSL Q FPDDDYSW WDLFMKICVF IFAFVIPVLI IIVCYTLMIL RLKSVRLLSG SREKDRNLRR ITRLVLVVVA VFVVCWTPIH IF ILVEALG STSHSTAALS SYYFCIALGY TNSCLNPILY AFLDENFKRC FRDFCFPLKM RMERQSTSRV RNTARGRTPP SLG PQDESC (TPO)(TPO)A(SEP)(SEP)(SEP)LAKD TSSGG

UniProtKB: Kappa-type opioid receptor, Vasopressin V2 receptor

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Macromolecule #4: Fab30 heavy chain

MacromoleculeName: Fab30 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.754586 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSAASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSAASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK TGSHHHHHHH HG G

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Macromolecule #5: Fab30 light chain

MacromoleculeName: Fab30 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #6: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(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
type: ligand / ID: 6 / Number of copies: 1 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

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

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Macromolecule #7: N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-...

MacromoleculeName: N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: CVV
Molecular weightTheoretical: 554.419 Da
Chemical component information

ChemComp-CVV:
N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 16000 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number images used: 163293
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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