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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


TGFBR3 regulates TGF-beta signaling / oculomotor nerve development / MAP2K and MAPK activation / Activation of SMO / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / regulation of actin polymerization or depolymerization / telencephalon cell migration ...TGFBR3 regulates TGF-beta signaling / oculomotor nerve development / MAP2K and MAPK activation / Activation of SMO / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / regulation of actin polymerization or depolymerization / telencephalon cell migration / positive regulation of mesenchymal stem cell migration / C-X-C chemokine binding / chemokine receptor binding / response to ultrasound / CXCL12-activated CXCR4 signaling pathway / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / 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 / positive regulation of vasculature development / desensitization of G protein-coupled receptor signaling pathway / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / Clathrin-mediated endocytosis / C-C chemokine receptor activity / integrin activation / negative regulation of dendritic cell apoptotic process / clathrin-dependent endocytosis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / chemokine-mediated signaling pathway / cellular response to chemokine / C-C chemokine binding / G protein-coupled receptor internalization / acetylcholine receptor binding / positive regulation of monocyte chemotaxis / inositol hexakisphosphate binding / chemokine activity / Chemokine receptors bind chemokines / blood circulation / Thrombin signalling through proteinase activated receptors (PARs) / scavenger receptor activity / G alpha (s) signalling events / clathrin binding / positive regulation of calcium ion import / small molecule binding / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / detection of temperature stimulus involved in sensory perception of pain / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / animal organ regeneration / positive regulation of T cell migration / detection of mechanical stimulus involved in sensory perception of pain / vasculogenesis / Nuclear signaling by ERBB4 / coreceptor activity / clathrin-coated pit / positive regulation of endothelial cell proliferation / positive regulation of cell adhesion / positive regulation of neuron differentiation / axon guidance / adult locomotory behavior / cell chemotaxis / growth factor activity / G protein-coupled receptor binding / calcium-mediated signaling / defense response / recycling endosome / response to virus / receptor internalization / response to peptide hormone / intracellular calcium ion homeostasis / neuron migration / chemotaxis / integrin binding / protein transport / positive regulation of protein phosphorylation / positive regulation of cytosolic calcium ion concentration / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / : / G alpha (i) signalling events / angiogenesis / molecular adaptor activity / Estrogen-dependent gene expression / early endosome / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / endosome / cell adhesion / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding
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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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: To Be Published
Title: ACKR3-arrestin2/3 complexes reveal molecular consequences of GRK-dependent barcoding
Authors: Chen, Q. / Tesmer, J.J.G.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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