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

Validation slider image for 9E82

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 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.

Macromolecule Content 

  • Total Structure Weight: 150.18 kDa 
  • Atom Count: 8,200 
  • Modeled Residue Count: 1,034 
  • Deposited Residue Count: 1,335 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  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
Find similar proteins by:|  3D Structure
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48061
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab7 heavy chainC [auth H]240synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab7 light chainD [auth L]215synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25106
Sequence Annotations
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Reference Sequence

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