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- EMDB-39423: Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 i... -

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Basic information

Entry
Database: EMDB / ID: EMD-39423
TitleStructure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
Map data
Sample
  • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
    • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1
      • Protein or peptide: Atypical chemokine receptor 1
    • Complex: CXCL8
      • Protein or peptide: IL-8(9-77)
KeywordsGPCR / SIGNALING PROTEIN / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of chemokine production / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis ...regulation of chemokine production / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis / chemokine-mediated signaling pathway / C-C chemokine binding / positive regulation of neutrophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / negative regulation of G protein-coupled receptor signaling pathway / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / cellular response to fibroblast growth factor stimulus / neutrophil chemotaxis / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / calcium-mediated signaling / response to molecule of bacterial origin / G protein-coupled receptor activity / defense response / recycling endosome / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / transmembrane signaling receptor activity / signaling receptor activity / heparin binding / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / G alpha (i) signalling events / early endosome / intracellular signal transduction / G protein-coupled receptor signaling pathway / inflammatory response / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Duffy antigen/chemokine receptor / CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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
Similarity search - Domain/homology
Interleukin-8 / Atypical chemokine receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsBanerjee R / Khanppnavar B / Maharana J / Saha S / Korkhov VM / Shukla AK
Funding support India, United Kingdom, 4 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR29041/BRB/10/1697/2018 India
Wellcome TrustIA/S/20/1/504916 United Kingdom
Science and Engineering Research Board (SERB)SPR/2020/000408 India
Science and Engineering Research Board (SERB)IPA/2020/000405 India
CitationJournal: To Be Published
Title: Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
Authors: Banerjee R / Khanppnavar B / Maharana J / Saha S / Korkhov VM / Shukla AK
History
DepositionMar 11, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39423.png

Downloads & links

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Map

FileDownload / File: emd_39423.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 288 pix.
= 270.4 Å		0.94 Å/pix.
x 288 pix.
= 270.4 Å		0.94 Å/pix.
x 288 pix.
= 270.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.289
Minimum - Maximum-2.6444628 - 3.0738502
Average (Standard dev.)-0.0016421945 (±0.052259292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 270.40033 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39423_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_39423_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex wit...

EntireName: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
Components
  • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
    • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1
      • Protein or peptide: Atypical chemokine receptor 1
    • Complex: CXCL8
      • Protein or peptide: IL-8(9-77)

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Supramolecule #1: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex wit...

SupramoleculeName: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1

SupramoleculeName: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: CXCL8

SupramoleculeName: CXCL8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Atypical chemokine receptor 1

MacromoleculeName: Atypical chemokine receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.524102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKTIIALSY IFCLVFADYK DDDYAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSGNC LHRAELSPST ENSSQLDFED VWNSSYGVN DSFPDGDYGA NLEAAAPCHS CNLLDDSALP FFILTSVLGI LASSTVLFML FRPLFRWQLC PGWPVLAQLA V GSALFSIV ...String:
MGKTIIALSY IFCLVFADYK DDDYAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSGNC LHRAELSPST ENSSQLDFED VWNSSYGVN DSFPDGDYGA NLEAAAPCHS CNLLDDSALP FFILTSVLGI LASSTVLFML FRPLFRWQLC PGWPVLAQLA V GSALFSIV VPVLAPGLGS TRSSALCSLG YCVWYGSAFA QALLLGCHAS LGHRLGAGQV PGLTLGLTVG IWGVAALLTL PV TLASGAS GGLCTLIYST ELKALQATHT VACLAIFVLL PLGLFGAKGL KKALGMGPGP WMNILWAWFI FWWPHGVVLG LDF LVRSKL LLLSTCLAQQ ALDLLLNLAE ALAILHCVAT PLLLALFCHQ ATRTLLPSLP LPEGWSSHLD TLGSKS

UniProtKB: Atypical chemokine receptor 1

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Macromolecule #2: IL-8(9-77)

MacromoleculeName: IL-8(9-77) / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.125646 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EGAVLPRSAK ELRCQCIKTY SKPFHPKFIK ELRVIESGPH CANTEIIVKL SDGRELCLDP KENWVQRVVE KFLKRAENS

UniProtKB: Interleukin-8

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 26196039
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8jps

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 473012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8jps


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ynf:
Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8

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