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

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Basic information

Entry
Database: PDB / ID: 8jps
TitleStructure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Composite map)
Components
  • Atypical chemokine receptor 1
  • C-C motif chemokine 7
KeywordsIMMUNE SYSTEM / GPCR / SIGNALING PROTEIN
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 / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines ...regulation of chemokine production / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cytoskeleton organization / Peptide ligand-binding receptors / response to gamma radiation / G protein-coupled receptor activity / recycling endosome / defense response / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / transmembrane signaling receptor activity / cell-cell signaling / signaling receptor activity / heparin binding / regulation of cell shape / early endosome / positive regulation of cell migration / inflammatory response / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Duffy antigen/chemokine receptor / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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
C-C motif chemokine 7 / 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: Cell / Year: 2024
Title: Molecular mechanism of distinct chemokine engagement and functional divergence of the human Duffy antigen receptor.
Authors: Shirsha Saha / Basavraj Khanppnavar / Jagannath Maharana / Heeryung Kim / Carlo Marion C Carino / Carole Daly / Shane Houston / Saloni Sharma / Nashrah Zaidi / Annu Dalal / Sudha Mishra / ...Authors: Shirsha Saha / Basavraj Khanppnavar / Jagannath Maharana / Heeryung Kim / Carlo Marion C Carino / Carole Daly / Shane Houston / Saloni Sharma / Nashrah Zaidi / Annu Dalal / Sudha Mishra / Manisankar Ganguly / Divyanshu Tiwari / Poonam Kumari / Gagan Deep Jhingan / Prem N Yadav / Bianca Plouffe / Asuka Inoue / Ka Young Chung / Ramanuj Banerjee / Volodymyr M Korkhov / Arun K Shukla /
Abstract: The Duffy antigen receptor is a seven-transmembrane (7TM) protein expressed primarily at the surface of red blood cells and displays strikingly promiscuous binding to multiple inflammatory and ...The Duffy antigen receptor is a seven-transmembrane (7TM) protein expressed primarily at the surface of red blood cells and displays strikingly promiscuous binding to multiple inflammatory and homeostatic chemokines. It serves as the basis of the Duffy blood group system in humans and also acts as the primary attachment site for malarial parasite Plasmodium vivax and pore-forming toxins secreted by Staphylococcus aureus. Here, we comprehensively profile transducer coupling of this receptor, discover potential non-canonical signaling pathways, and determine the cryoelectron microscopy (cryo-EM) structure in complex with the chemokine CCL7. The structure reveals a distinct binding mode of chemokines, as reflected by relatively superficial binding and a partially formed orthosteric binding pocket. We also observe a dramatic shortening of TM5 and 6 on the intracellular side, which precludes the formation of the docking site for canonical signal transducers, thereby providing a possible explanation for the distinct pharmacological and functional phenotype of this receptor.
History
DepositionJun 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Sep 4, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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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: C-C motif chemokine 7
A: Atypical chemokine receptor 1
C: C-C motif chemokine 7


Theoretical massNumber of molelcules
Total (without water)71,3374
Polymers71,3374
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


Mass: 28073.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACKR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16570
#2: Protein C-C motif chemokine 7 / Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small- ...Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small-inducible cytokine A7


Mass: 7594.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL7, MCP3, SCYA6, SCYA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80098
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, CCL7COMPLEXall0RECOMBINANT
2Duffy Antigen Receptor for Chemokines (DARC)/ACKR1COMPLEX#11RECOMBINANT
3CCL7COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Escherichia 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: 58 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
9PHENIX1.20.1model refinement
13cryoSPARC43D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 25479169
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 308174 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.014862
ELECTRON MICROSCOPYf_angle_d0.9936652
ELECTRON MICROSCOPYf_dihedral_angle_d5.102660
ELECTRON MICROSCOPYf_chiral_restr0.046817
ELECTRON MICROSCOPYf_plane_restr0.009805

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