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Yorodumi- EMDB-36488: Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36488 | |||||||||||||||
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Title | Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Composite map) | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | GPCR / SIGNALING PROTEIN / IMMUNE SYSTEM | |||||||||||||||
Function / homology | Function and homology information regulation of chemokine production / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway ...regulation of chemokine production / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / cytoskeleton organization / Peptide ligand-binding receptors / neutrophil chemotaxis / G protein-coupled receptor activity / response to gamma radiation / recycling endosome / defense response / cellular response to type II interferon / intracellular calcium ion homeostasis / transmembrane signaling receptor activity / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / signaling receptor activity / heparin binding / regulation of cell shape / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.65 Å | |||||||||||||||
Authors | Banerjee R / Khanppnavar B / Maharana J / Saha S / Korkhov VM / Shukla AK | |||||||||||||||
Funding support | India, United Kingdom, 4 items
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Citation | Journal: Cell(Cambridge,Mass.) / Year: 2024 Title: Molecular mechanism of distinct chemokine engagement and functional divergence of the human Duffy antigen receptor Authors: Saha S / Khanppnavar B / Maharana J / Kim H / Carino CMC / Daly C / Houston S / Sharma S / Zaidi N / Dalal A / Mishra S / Ganguly M / Tiwari D / Kumari P / Jhingan GD / Yadav PN / Plouffe B ...Authors: Saha S / Khanppnavar B / Maharana J / Kim H / Carino CMC / Daly C / Houston S / Sharma S / Zaidi N / Dalal A / Mishra S / Ganguly M / Tiwari D / Kumari P / Jhingan GD / Yadav PN / Plouffe B / Inoue A / Chung KY / Banerjee R / Korkhov VM / Shukla AK | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36488.map.gz | 77.7 MB | EMDB map data format | |
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Header (meta data) | emd-36488-v30.xml emd-36488.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36488_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_36488.png | 44.9 KB | ||
Filedesc metadata | emd-36488.cif.gz | 6.1 KB | ||
Others | emd_36488_half_map_1.map.gz emd_36488_half_map_2.map.gz | 77.5 MB 77.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36488 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36488 | HTTPS FTP |
-Validation report
Summary document | emd_36488_validation.pdf.gz | 765.7 KB | Display | EMDB validaton report |
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Full document | emd_36488_full_validation.pdf.gz | 765.2 KB | Display | |
Data in XML | emd_36488_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_36488_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36488 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36488 | HTTPS FTP |
-Related structure data
Related structure data | 8jpsMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36488.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93889 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36488_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36488_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex wit...
Entire | Name: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 |
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Components |
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-Supramolecule #1: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex wit...
Supramolecule | Name: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1
Supramolecule | Name: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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-Supramolecule #3: CCL7
Supramolecule | Name: CCL7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Atypical chemokine receptor 1
Macromolecule | Name: Atypical chemokine receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.073523 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: EAAAPCHSCN LLDDSALPFF ILTSVLGILA SSTVLFMLFR PLFRWQLCPG WPVLAQLAVG SALFSIVVPV LAPGLGSTRS SALCSLGYC VWYGSAFAQA LLLGCHASLG HRLGAGQVPG LTLGLTVGIW GVAALLTLPV TLASGASGGL CTLIYSTELK A LQATHTVA ...String: EAAAPCHSCN LLDDSALPFF ILTSVLGILA SSTVLFMLFR PLFRWQLCPG WPVLAQLAVG SALFSIVVPV LAPGLGSTRS SALCSLGYC VWYGSAFAQA LLLGCHASLG HRLGAGQVPG LTLGLTVGIW GVAALLTLPV TLASGASGGL CTLIYSTELK A LQATHTVA CLAIFVLLPL GLFGAKGLKK ALGMGPGPWM NILWAWFIFW WPHGVVLGLD FLVRSKLLLL STCLAQQALD LL LNLAEAL AILHCVATPL LLALFCHQAT UniProtKB: Atypical chemokine receptor 1 |
-Macromolecule #2: C-C motif chemokine 7
Macromolecule | Name: C-C motif chemokine 7 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.594902 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: STTCCYRFIN KKIPKQRLES YRRTTSSHCP REAVIFKTKL DKEICADPTQ KWVQDFMKHL DKK UniProtKB: C-C motif chemokine 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-8jps: |