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- EMDB-38742: Structure of CXCR2 bound to CXCL5 (Ligand-receptor focused map) -

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Basic information

Entry
Database: EMDB / ID: EMD-38742
TitleStructure of CXCR2 bound to CXCL5 (Ligand-receptor focused map)
Map data
Sample
  • Complex: C-X-C chemokine receptor type 2 in complex with C-X-C motif chemokine 5
    • Complex: C-X-C chemokine receptor type 2
      • Protein or peptide: C-X-C chemokine receptor type 2
    • Complex: C-X-C motif chemokine 5
      • Protein or peptide: C-X-C motif chemokine 5
KeywordsGPCR / Arrestin / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / neutrophil activation / C-C chemokine receptor activity / C-C chemokine binding / chemokine activity ...interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / neutrophil activation / C-C chemokine receptor activity / 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 / 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 / identical protein binding / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsSano FK / Saha S / Sharma S / Ganguly M / Shihoya W / Nureki O / Shukla AK / Banerjee R
Funding support India, 1 items
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, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38742.png

Downloads & links

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Map

FileDownload / File: emd_38742.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 440 pix.
= 464.816 Å		1.06 Å/pix.
x 440 pix.
= 464.816 Å		1.06 Å/pix.
x 440 pix.
= 464.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0564 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.34
Minimum - Maximum-37.298594999999999 - 78.154330000000002
Average (Standard dev.)0.000000000000288 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 464.81598 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38742_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38742_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 : C-X-C chemokine receptor type 2 in complex with C-X-C motif chemo...

EntireName: C-X-C chemokine receptor type 2 in complex with C-X-C motif chemokine 5
Components
  • Complex: C-X-C chemokine receptor type 2 in complex with C-X-C motif chemokine 5
    • Complex: C-X-C chemokine receptor type 2
      • Protein or peptide: C-X-C chemokine receptor type 2
    • Complex: C-X-C motif chemokine 5
      • Protein or peptide: C-X-C motif chemokine 5

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Supramolecule #1: C-X-C chemokine receptor type 2 in complex with C-X-C motif chemo...

SupramoleculeName: C-X-C chemokine receptor type 2 in complex with C-X-C motif chemokine 5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: C-X-C chemokine receptor type 2

SupramoleculeName: C-X-C chemokine receptor type 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: C-X-C motif chemokine 5

SupramoleculeName: C-X-C motif chemokine 5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

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Macromolecule #1: C-X-C motif chemokine 5

MacromoleculeName: C-X-C motif chemokine 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.367868 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGPAAAVLRE LRCVCLQTTQ GVHPKMISNL QVFAIGPQCS KVEVVASLKN GKEICLDPEA PFLKKVIQKI LDGGNKEN

UniProtKB: C-X-C motif chemokine 5

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Macromolecule #2: C-X-C chemokine receptor type 2

MacromoleculeName: C-X-C chemokine receptor type 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.699609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSEDF NMESDSFEDF WKGEDLSNYS YSSTLPPFL LDAAPCEPES LEINKYFVVI IYALVFLLSL LGNSLVMLVI LYSRVGRSVT DVYLLNLALA DLLFALTLPI W AASKVNGW ...String:
MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSEDF NMESDSFEDF WKGEDLSNYS YSSTLPPFL LDAAPCEPES LEINKYFVVI IYALVFLLSL LGNSLVMLVI LYSRVGRSVT DVYLLNLALA DLLFALTLPI W AASKVNGW IFGTFLCKVV SLLKEVNFYS GILLLACISV DRYLAIVHAT RTLTQKRYLV KFICLSIWGL SLLLALPVLL FR RTVYSSN VSPACYEDMG NNTANWRMLL RILPQSFGFI VPLLIMLFCY GFTLRTLFKA HMGQKHRAMR VIFAVVLIFL LCW LPYNLV LLADTLMRTQ VIQETCERRN HIDRALDATE ILGILHSCLN PLIYAFIGQK FRHGLLKILA IHGLISKDSL PKDS RPSFV GSSSGHTSTT L

UniProtKB: C-X-C chemokine receptor type 2

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 50.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2047293
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 4.4), RELION (ver. 4)) / Number images used: 131780
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8xws:
Structure of CXCR2 bound to CXCL5 (Ligand-receptor focused map)

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