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- PDB-9e82: ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7 -

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Basic information

Entry
Database: PDB / ID: 9.0E+82
TitleACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7
Components
  • Atypical chemokine receptor 3
  • Beta-arrestin-1
  • Fab7 heavy chain
  • Fab7 light chain
  • SDF-1-beta(3-72)
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / complex / GPCR / arrestin / signaling / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


oculomotor nerve development / TGFBR3 regulates TGF-beta signaling / positive regulation of mesenchymal stem cell migration / telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / MAP2K and MAPK activation / response to ultrasound / Activation of SMO / negative regulation of leukocyte tethering or rolling / Golgi Associated Vesicle Biogenesis ...oculomotor nerve development / TGFBR3 regulates TGF-beta signaling / positive regulation of mesenchymal stem cell migration / telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / MAP2K and MAPK activation / response to ultrasound / Activation of SMO / negative regulation of leukocyte tethering or rolling / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / regulation of actin polymerization or depolymerization / C-X-C chemokine binding / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / positive regulation of axon extension involved in axon guidance / Cargo recognition for clathrin-mediated endocytosis / clathrin heavy chain binding / positive regulation of vasculature development / Signaling by ROBO receptors / induction of positive chemotaxis / Clathrin-mediated endocytosis / negative regulation of dendritic cell apoptotic process / integrin activation / positive regulation of dopamine secretion / clathrin-dependent endocytosis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to chemokine / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / C-C chemokine binding / acetylcholine receptor binding / positive regulation of monocyte chemotaxis / G protein-coupled receptor internalization / inositol hexakisphosphate binding / chemokine activity / sensory perception / Chemokine receptors bind chemokines / blood circulation / scavenger receptor activity / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / small molecule binding / positive regulation of calcium ion import / phosphatidylinositol-3,4,5-trisphosphate binding / detection of temperature stimulus involved in sensory perception of pain / pseudopodium / positive regulation of receptor internalization / animal organ regeneration / negative regulation of Notch signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of T cell migration / vasculogenesis / Nuclear signaling by ERBB4 / coreceptor activity / positive regulation of endothelial cell proliferation / clathrin-coated pit / positive regulation of neuron differentiation / positive regulation of cell adhesion / axon guidance / chemokine-mediated signaling pathway / adult locomotory behavior / cell chemotaxis / growth factor activity / calcium-mediated signaling / defense response / positive regulation of protein phosphorylation / receptor internalization / G protein-coupled receptor binding / recycling endosome / response to peptide hormone / integrin binding / response to virus / neuron migration / chemotaxis / intracellular calcium ion homeostasis / protein transport / positive regulation of cytosolic calcium ion concentration / extracellular matrix / cytoplasmic vesicle / angiogenesis / G alpha (i) signalling events / Estrogen-dependent gene expression / molecular adaptor activity / ubiquitin-dependent protein catabolic process / early endosome / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / cell adhesion / endosome / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation
Similarity search - Function
Atypical chemokine receptor 3 / : / CXC Chemokine domain / 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 ...Atypical chemokine receptor 3 / : / CXC Chemokine domain / 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 / Arrestin-like, C-terminal / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Immunoglobulin E-set
Similarity search - Domain/homology
CHOLESTEROL / Beta-arrestin-1 / Atypical chemokine receptor 3 / Stromal cell-derived factor 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen, Q. / Fuller, J. / Tesmer, J.J.G.
Funding support United States, Denmark, 12items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA254402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161880 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA221289 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA023168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137505 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA023168 United States
Walther Cancer Foundation United States
The Robertson FoundationIrvington Postdoctoral Fellowship United States
Villum Fonden00025326 Denmark
Ralph W. and Grace M. Showalter Research Trust4480108 United States
CitationJournal: Nature / Year: 2025
Title: Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor.
Authors: Qiuyan Chen / Christopher T Schafer / Somnath Mukherjee / Kai Wang / Martin Gustavsson / James R Fuller / Katelyn Tepper / Thomas D Lamme / Yasmin Aydin / Parth Agrawal / Genki Terashi / Xin- ...Authors: Qiuyan Chen / Christopher T Schafer / Somnath Mukherjee / Kai Wang / Martin Gustavsson / James R Fuller / Katelyn Tepper / Thomas D Lamme / Yasmin Aydin / Parth Agrawal / Genki Terashi / Xin-Qiu Yao / Daisuke Kihara / Anthony A Kossiakoff / Tracy M Handel / John J G Tesmer /
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 ...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, 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. ). 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.
History
DepositionNov 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
B: SDF-1-beta(3-72)
H: Fab7 heavy chain
L: Fab7 light chain
R: Atypical chemokine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1806
Polymers149,7935
Non-polymers3871
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 , 3 types, 3 molecules ABR

#1: Protein Beta-arrestin-1 / Arrestin beta-1 / Arrestin-2


Mass: 47055.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P17870
#2: Protein SDF-1-beta(3-72)


Mass: 8189.663 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / References: UniProt: P48061
#5: Protein Atypical chemokine receptor 3 / C-X-C chemokine receptor type 7 / CXC-R7 / CXCR-7 / Chemokine orphan receptor 1 / G-protein coupled ...C-X-C chemokine receptor type 7 / CXC-R7 / CXCR-7 / Chemokine orphan receptor 1 / G-protein coupled receptor 159 / G-protein coupled receptor RDC1 homolog / RDC-1


Mass: 45356.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACKR3, CMKOR1, CXCR7, GPR159, RDC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25106

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab7 heavy chain


Mass: 25720.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab7 light chain


Mass: 23471.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has ligand of interestN
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: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)Organism: Bos taurus (domestic cattle)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104555 / Symmetry type: POINT

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