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- PDB-8xwm: Structure of CXCR2 bound to CXCL6 (Ligand-receptor focused map) -

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Basic information

Entry
Database: PDB / ID: 8xwm
TitleStructure of CXCR2 bound to CXCL6 (Ligand-receptor focused map)
Components
  • C-X-C chemokine receptor type 2
  • C-X-C motif chemokine 6
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of neutrophil mediated killing of gram-negative bacterium / regulation of chemokine production / leukocyte homeostasis / interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / antibacterial innate immune response / CXCR chemokine receptor binding / C-X-C chemokine receptor activity ...regulation of neutrophil mediated killing of gram-negative bacterium / regulation of chemokine production / leukocyte homeostasis / interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / antibacterial innate immune response / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / neutrophil activation / C-C chemokine receptor activity / chemokine-mediated signaling pathway / C-C chemokine binding / chemokine activity / Chemokine receptors bind chemokines / dendritic cell chemotaxis / cellular defense response / neutrophil chemotaxis / secretory granule membrane / calcium-mediated signaling / G protein-coupled receptor activity / receptor internalization / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / mitotic spindle / cell-cell signaling / heparin binding / cellular response to lipopolysaccharide / microtubule cytoskeleton / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane
Similarity search - Function
CXC chemokine receptor 2 / CXC chemokine receptor 1/2 / 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 ...CXC chemokine receptor 2 / CXC chemokine receptor 1/2 / 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 / 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)
Similarity search - Domain/homology
C-X-C chemokine receptor type 2 / C-X-C motif chemokine 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsSano, F.K. / Saha, S. / Sharma, S. / Ganguly, M. / Shihoya, W. / Nureki, O. / Shukla, A.K. / Banerjee, R.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)IPA/2020/000405 India
CitationJournal: Mol Cell / Year: 2025
Title: Molecular basis of promiscuous chemokine binding and structural mimicry at the C-X-C chemokine receptor, CXCR2.
Authors: Shirsha Saha / Fumiya K Sano / Saloni Sharma / Manisankar Ganguly / Sudha Mishra / Annu Dalal / Hiroaki Akasaka / Takaaki A Kobayashi / Nashrah Zaidi / Divyanshu Tiwari / Nabarun Roy / ...Authors: Shirsha Saha / Fumiya K Sano / Saloni Sharma / Manisankar Ganguly / Sudha Mishra / Annu Dalal / Hiroaki Akasaka / Takaaki A Kobayashi / Nashrah Zaidi / Divyanshu Tiwari / Nabarun Roy / Manish K Yadav / Nilanjana Banerjee / Sayantan Saha / Samanwita Mohapatra / Yuzuru Itoh / Andy Chevigné / Ramanuj Banerjee / Wataru Shihoya / Osamu Nureki / Arun K Shukla /
Abstract: Selectivity of natural agonists for their cognate receptors is a hallmark of G-protein-coupled receptors (GPCRs); however, this selectivity often breaks down at the chemokine receptors. Chemokines ...Selectivity of natural agonists for their cognate receptors is a hallmark of G-protein-coupled receptors (GPCRs); however, this selectivity often breaks down at the chemokine receptors. Chemokines often display promiscuous binding to chemokine receptors, but the underlying molecular determinants remain mostly elusive. Here, we perform a comprehensive transducer-coupling analysis, testing all known C-X-C chemokines on every C-X-C type chemokine receptor to generate a global fingerprint of the selectivity and promiscuity encoded within this system. Taking lead from this, we determine cryoelectron microscopy (cryo-EM) structures of the most promiscuous receptor, C-X-C chemokine receptor 2 (CXCR2), in complex with several chemokines. These structural snapshots elucidate the details of ligand-receptor interactions, including structural motifs, which are validated using mutagenesis and functional experiments. We also observe that most chemokines position themselves on CXCR2 as a dimer while CXCL6 exhibits a monomeric binding pose. Taken together, our findings provide the molecular basis of chemokine promiscuity at CXCR2 with potential implications for developing therapeutic molecules.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: C-X-C motif chemokine 6
R: C-X-C chemokine receptor type 2


Theoretical massNumber of molelcules
Total (without water)55,0292
Polymers55,0292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein C-X-C motif chemokine 6 / Chemokine alpha 3 / CKA-3


Mass: 8328.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL6 / Production host: Escherichia coli (E. coli) / References: UniProt: P80162
#2: Protein C-X-C chemokine receptor type 2 / CXC-R2 / CXCR-2


Mass: 46699.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25025
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
1C-X-C chemokine receptor type 2 in complex with C-X-C motif chemokine 6COMPLEXall0RECOMBINANT
2C-X-C chemokine receptor type 2COMPLEX#21RECOMBINANT
3C-X-C motif chemokine 6COMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Escherichia 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
4cryoSPARC4.4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
12cryoSPARC4.4classification
13cryoSPARC4.43D reconstruction
14RELION43D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1609421
3D reconstructionResolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61539 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: SwissModel / Type: in silico model

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