9ZZO | pdb_00009zzo

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

• PDB DOI: https://doi.org/10.2210/pdb9ZZO/pdb
• EM Map EMD-75011: EMDB EMDataResource

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Lama glama, Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2026-01-07 Released: 2026-06-17 
• Deposition Author(s): Han, J., Chen, M., Che, T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural dynamics of kappa opioid receptor interactions with beta-arrestin 1.

Han, J., Fine, E.J., Jiang, Q., Zhuang, Y., Suomivuori, C.M., Chen, Z.W., Denn, E., Whiddon, K., Li, K., Evers, A.S., Fuller, J., Carter, J., Fay, J.F., Chen, M., Dror, R.O., Che, T.

(2026) Nat Commun 

• PubMed: 42243110 
• DOI: https://doi.org/10.1038/s41467-026-73968-3
• Primary Citation Related Structures: 
  9ZZO


• PubMed 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 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.

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Organizational Affiliation: 
• Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA. [e-mail].
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Department of Computer Science, Stanford University, Stanford, CA, USA.
Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
Department of Structural Biology, Stanford University, Stanford, CA, USA.
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
Division of Basic Research, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA.
Helix Biostructures, Indianapolis, IN, USA.
Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD, USA.
SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 146.24 kDa 
• Atom Count: 8,637 
• Modeled Residue Count: 1,147 
• Deposited Residue Count: 1,308 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 32	A [auth E]	124	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1B of Beta-arrestin-1	B [auth C]	387	Homo sapiens	Mutation(s): 0  Gene Names: ARRB1, ARR1
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens) Go to UniProtKB:  P49407
PHAROS:  P49407 GTEx:  ENSG00000137486

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa-type opioid receptor,Vasopressin V2 receptor	C [auth A]	341	Homo sapiens	Mutation(s): 0  Gene Names: OPRK1, OPRK, AVPR2, ADHR, DIR, DIR3, V2R
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens) Explore P41145  Go to UniProtKB:  P41145
PHAROS:  P41145 GTEx:  ENSG00000082556
Find proteins for P30518 (Homo sapiens) Explore P30518  Go to UniProtKB:  P30518
PHAROS:  P30518 GTEx:  ENSG00000126895
UniProt Groups	P41145P30518

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab30 heavy chain	D [auth H]	241	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab30 light chain	E [auth L]	215	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PIO	F [auth C]	[(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 C25 H49 O19 P3 XLNCEHRXXWQMPK-MJUMVPIBSA-N
CVV (Subject of Investigation/LOI)	G [auth A]	N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide C27 H27 I N2 O3 WTIFKSFIQUZRRN-JXGKSYOJSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C [auth A]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	C [auth A]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-17 
Deposition Author(s): Han, J., Chen, M., Che, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM143061

Revision History  

• Version 1.0: 2026-06-17
  Type: Initial release