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- EMDB-47700: ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7 -

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Basic information

Entry
Database: EMDB / ID: EMD-47700
TitleACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7
Map data
Sample
  • Complex: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: SDF-1-beta(3-72)
    • Protein or peptide: Fab7 heavy chain
    • Protein or peptide: Fab7 light chain
    • Protein or peptide: Atypical chemokine receptor 3
  • Ligand: CHOLESTEROL
Keywordscomplex / GPCR / arrestin / signaling / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


TGFBR3 regulates TGF-beta signaling / oculomotor nerve development / positive regulation of mesenchymal stem cell migration / MAP2K and MAPK activation / Activation of SMO / telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / Golgi Associated Vesicle Biogenesis / negative regulation of leukocyte tethering or rolling / response to ultrasound ...TGFBR3 regulates TGF-beta signaling / oculomotor nerve development / positive regulation of mesenchymal stem cell migration / MAP2K and MAPK activation / Activation of SMO / telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / Golgi Associated Vesicle Biogenesis / negative regulation of leukocyte tethering or rolling / response to ultrasound / Lysosome Vesicle Biogenesis / regulation of actin polymerization or depolymerization / chemokine receptor binding / C-X-C chemokine binding / AP-2 adaptor complex binding / CXCL12-activated CXCR4 signaling pathway / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / CXCR chemokine receptor binding / Cargo recognition for clathrin-mediated endocytosis / C-X-C chemokine receptor activity / positive regulation of axon extension involved in axon guidance / desensitization of G protein-coupled receptor signaling pathway / positive regulation of vasculature development / positive regulation of dopamine secretion / Signaling by ROBO receptors / Clathrin-mediated endocytosis / induction of positive chemotaxis / integrin activation / clathrin-dependent endocytosis / negative regulation of dendritic cell apoptotic process / C-C chemokine receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to chemokine / chemokine-mediated signaling pathway / C-C chemokine binding / acetylcholine receptor binding / G protein-coupled receptor internalization / positive regulation of monocyte chemotaxis / inositol hexakisphosphate binding / chemokine activity / blood circulation / Chemokine receptors bind chemokines / 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 / pseudopodium / detection of temperature stimulus involved in sensory perception of pain / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / animal organ regeneration / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of T cell migration / vasculogenesis / Nuclear signaling by ERBB4 / coreceptor activity / clathrin-coated pit / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / positive regulation of cell adhesion / axon guidance / adult locomotory behavior / cell chemotaxis / growth factor activity / calcium-mediated signaling / defense response / G protein-coupled receptor binding / response to peptide hormone / recycling endosome / receptor internalization / response to virus / integrin binding / positive regulation of protein phosphorylation / neuron migration / intracellular calcium ion homeostasis / chemotaxis / protein transport / : / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / angiogenesis / G alpha (i) signalling events / molecular adaptor activity / Estrogen-dependent gene expression / 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 / signaling receptor binding / negative regulation of cell population proliferation
Similarity search - Function
Atypical chemokine receptor 3 / : / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / CXC Chemokine domain / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain ...Atypical chemokine receptor 3 / : / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / CXC Chemokine domain / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen Q / Fuller J / Tesmer JJG
Funding support United States, Denmark, 12 items
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, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47700.png

Downloads & links

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Map

FileDownload / File: emd_47700.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 404.736 Å		1.05 Å/pix.
x 384 pix.
= 404.736 Å		1.05 Å/pix.
x 384 pix.
= 404.736 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.148
Minimum - Maximum-1.3723519 - 1.9638036
Average (Standard dev.)0.00021634834 (±0.012477437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 404.73642 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47700_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47700_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : human ACKR3 phosphorylated by GRK5 in complex with Arrestin3

EntireName: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
Components
  • Complex: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: SDF-1-beta(3-72)
    • Protein or peptide: Fab7 heavy chain
    • Protein or peptide: Fab7 light chain
    • Protein or peptide: Atypical chemokine receptor 3
  • Ligand: CHOLESTEROL

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Supramolecule #1: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3

SupramoleculeName: human ACKR3 phosphorylated by GRK5 in complex with Arrestin3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 47.055469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI RKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP EHETPVDTNL IELDTNDDDA AAEDFARQRL KGMK DDKEE EEDGTGSPRL NDR

UniProtKB: Beta-arrestin-1

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Macromolecule #2: SDF-1-beta(3-72)

MacromoleculeName: SDF-1-beta(3-72) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.189663 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LRHQSLSYRC PCRFFESHVA RANVKHLKIL NTPNCALQIV ARLKNNNRQV CIDPKLKWIQ EYLEKALNK

UniProtKB: Stromal cell-derived factor 1

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Macromolecule #3: Fab7 heavy chain

MacromoleculeName: Fab7 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.720758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSSYIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARKSMYHRGW GWLSWVYGAM DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSSYIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARKSMYHRGW GWLSWVYGAM DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HT

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Macromolecule #4: Fab7 light chain

MacromoleculeName: Fab7 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.471031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYYYPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYYYPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #5: Atypical chemokine receptor 3

MacromoleculeName: Atypical chemokine receptor 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.356367 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAPDLHLFDY SEPGNFSDIS WPCNSSDCIV VDTVMCPNMP NKSVLLYTLS FIYIFIFVIG MIANSVVVWV NIQAKTTGYD THCYILNLA IADLWVVLTI PVWVVSLVQH NQWPMGELTC KVTHLIFSIN LFGSIFFLTC MSVDRYLSIT YFTNTPSSRK K MVRRVVCI ...String:
GAPDLHLFDY SEPGNFSDIS WPCNSSDCIV VDTVMCPNMP NKSVLLYTLS FIYIFIFVIG MIANSVVVWV NIQAKTTGYD THCYILNLA IADLWVVLTI PVWVVSLVQH NQWPMGELTC KVTHLIFSIN LFGSIFFLTC MSVDRYLSIT YFTNTPSSRK K MVRRVVCI LVWLLAFCVS LPDTYYLKTV TSASNNETYC RSFYPEHSIK EWLIGMELVS VVLGFAVPFS IIAVFYFLLA RA ISASSDQ EKHSSRKIIF SYVVVFLVCW LPYHVAVLLD IFSILHYIPF TCRLEHALFT ALHVTQCLSL VHCCVNPVLY SFI NRNYRY ELMKAFIFKY SAK(TPO)GL(TPO)KLI DASRVSETEY SALEQSTKGR PLEVLFQGPH HHHHHHHHHD YKDDDD K

UniProtKB: Atypical chemokine receptor 3

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104555
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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