9E82 | pdb_00009e82

ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7

  • Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
  • Organism(s): Bos taurus, Homo sapiens, synthetic construct
  • Expression System: Escherichia coli, Spodoptera frugiperda
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2024-11-04 Released: 2025-04-02 
  • Deposition Author(s): Chen, Q., Fuller, J., Tesmer, J.J.G.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Walther Cancer Foundation, The Robertson Foundation, Villum Fonden, Ralph W. and Grace M. Showalter Research Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor.

Chen, Q.Schafer, C.T.Mukherjee, S.Wang, K.Gustavsson, M.Fuller, J.R.Tepper, K.Lamme, T.D.Aydin, Y.Agrawal, P.Terashi, G.Yao, X.Q.Kihara, D.Kossiakoff, A.A.Handel, T.M.Tesmer, J.J.G.

(2025) Nature 643: 280-287

  • DOI: https://doi.org/10.1038/s41586-025-09024-9
  • Primary Citation of Related Structures:  
    8TII, 8TIL, 8TIN, 8TIO, 8VJ9, 9E82

  • PubMed Abstract: 

    Unique phosphorylation 'barcodes' installed in different regions of an active seven-transmembrane receptor by different G-protein-coupled receptor (GPCR) kinases (GRKs) have been proposed to promote distinct cellular outcomes 1 , but it is unclear whether or how arrestins differentially engage these barcodes. Here, to address this, we developed an antigen-binding fragment (Fab7) that recognizes both active arrestin2 (β-arrestin1) and arrestin3 (β-arrestin2) without interacting with bound receptor polypeptides. We used Fab7 to determine the structures of both arrestins in complex with atypical chemokine receptor 3 (ACKR3) phosphorylated in different regions of its C-terminal tail by either GRK2 or GRK5 (ref.  2 ). The GRK2-phosphorylated ACKR3 resulted in more heterogeneous 'tail-mode' assemblies, whereas phosphorylation by GRK5 resulted in more rigid 'ACKR3-adjacent' assemblies. Unexpectedly, the finger loops of both arrestins engaged the micelle surface rather than the receptor intracellular pocket, with arrestin3 being more dynamic, partly because of its lack of a membrane-anchoring motif. Thus, both the region of the barcode and the arrestin isoform involved can alter the structure and dynamics of GPCR-arrestin complexes, providing a possible mechanistic basis for unique downstream cellular effects, such as the efficiency of chemokine scavenging and the robustness of arrestin binding in ACKR3.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA. qch2@iu.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-1418Bos taurusMutation(s): 0 
Gene Names: ARRB1
Membrane Entity: Yes 
UniProt
Find proteins for P17870 (Bos taurus)
Explore P17870 
Go to UniProtKB:  P17870
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17870
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SDF-1-beta(3-72)69Homo sapiensMutation(s): 0 
Gene Names: CXCL12SDF1SDF1ASDF1B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens)
Explore P48061 
Go to UniProtKB:  P48061
PHAROS:  P48061
GTEx:  ENSG00000107562 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48061
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab7 heavy chainC [auth H]240synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab7 light chainD [auth L]215synthetic constructMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Atypical chemokine receptor 3E [auth R]393Homo sapiensMutation(s): 0 
Gene Names: ACKR3CMKOR1CXCR7GPR159RDC1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P25106 (Homo sapiens)
Explore P25106 
Go to UniProtKB:  P25106
PHAROS:  P25106
GTEx:  ENSG00000144476 
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UniProt GroupP25106
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
F [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
E [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA254402
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117372
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI161880
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA221289
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA023168
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137505
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL071818
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA023168
Walther Cancer FoundationUnited States--
The Robertson FoundationUnited StatesIrvington Postdoctoral Fellowship
Villum FondenDenmark00025326
Ralph W. and Grace M. Showalter Research TrustUnited States4480108

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Data collection, Database references