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- PDB-8ynf: Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 i... -

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Basic information

Entry
Database: PDB / ID: 8ynf
TitleStructure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
Components
  • Atypical chemokine receptor 1
  • IL-8(9-77)
KeywordsIMMUNE SYSTEM / GPCR / SIGNALING PROTEIN
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsBanerjee, R. / Khanppnavar, B. / Maharana, J. / Saha, S. / Korkhov, V.M. / Shukla, A.K.
Funding support India, United Kingdom, 4items
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, V.M. / Shukla, A.K.
History
DepositionMar 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 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

Downloads & links

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Assembly

Deposited unit
B: Atypical chemokine receptor 1
D: IL-8(9-77)
E: IL-8(9-77)
A: Atypical chemokine receptor 1
G: IL-8(9-77)
H: IL-8(9-77)


Theoretical massNumber of molelcules
Total (without water)119,5516
Polymers119,5516
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Atypical chemokine receptor 1 / Duffy antigen/chemokine receptor / Fy glycoprotein / GpFy / Glycoprotein D / Plasmodium vivax receptor


Mass: 41524.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACKR1, DARC, FY, GPD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16570
#2: Protein
IL-8(9-77) / GCP/IL-8 protein III / IL8/NAP1 form VI


Mass: 9125.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / Production host: Escherichia coli (E. coli) / References: UniProt: P10145
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

Component
IDNameTypeEntity IDParent-IDSource
1Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8COMPLEXall0RECOMBINANT
2Duffy Antigen Receptor for Chemokines (DARC)/ACKR1COMPLEX#11RECOMBINANT
3CXCL8COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 57.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
7Coot0.9.6model fitting
12cryoSPARC43D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 26196039
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 473012 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8JPS

8jps


Accession code: 8JPS / Source name: PDB / Type: experimental model

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