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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 / telencephalon cell migration / Activation of SMO / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / Golgi Associated Vesicle Biogenesis ...TGFBR3 regulates TGF-beta signaling / oculomotor nerve development / positive regulation of mesenchymal stem cell migration / MAP2K and MAPK activation / telencephalon cell migration / Activation of SMO / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / regulation of actin polymerization or depolymerization / chemokine receptor binding / C-X-C chemokine binding / 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 / clathrin-dependent endocytosis / negative regulation of dendritic cell apoptotic process / 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 / 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 / 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 / G protein-coupled receptor binding / defense response / recycling endosome / receptor internalization / response to peptide hormone / response to virus / positive regulation of protein phosphorylation / intracellular calcium ion homeostasis / neuron migration / chemotaxis / integrin binding / protein transport / positive regulation of cytosolic calcium ion concentration / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / : / angiogenesis / G alpha (i) signalling events / molecular adaptor activity / Estrogen-dependent gene expression / response to hypoxia / early endosome / positive regulation of ERK1 and ERK2 cascade / endosome / cell adhesion / 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 / : / 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
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: To Be Published
Title: ACKR3-arrestin2/3 complexes reveal molecular consequences of GRK-dependent barcoding
Authors: Chen Q / Tesmer JJG
History
DepositionNov 4, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 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

Slices (1/3)

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Slices (2/3)

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47700_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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

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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