[English] 日本語
Yorodumi
- PDB-8xvu: Structure of CXCR2 bound to CXCL2 (Ligand-receptor focused map) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xvu
TitleStructure of CXCR2 bound to CXCL2 (Ligand-receptor focused map)
Components
  • C-X-C chemokine receptor type 2
  • C-X-C motif chemokine 2
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


interleukin-8-mediated signaling pathway / metanephric tubule morphogenesis / negative regulation of neutrophil apoptotic process / mast cell granule / interleukin-8 receptor activity / interleukin-8 binding / acute inflammatory response to antigenic stimulus / C-X-C chemokine receptor activity / CXCR chemokine receptor binding / neutrophil activation ...interleukin-8-mediated signaling pathway / metanephric tubule morphogenesis / negative regulation of neutrophil apoptotic process / mast cell granule / interleukin-8 receptor activity / interleukin-8 binding / acute inflammatory response to antigenic stimulus / C-X-C chemokine receptor activity / CXCR chemokine receptor binding / neutrophil activation / C-C chemokine receptor activity / C-C chemokine binding / positive regulation of vascular permeability / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / dendritic cell chemotaxis / midbrain development / Interleukin-10 signaling / cellular defense response / positive regulation of cardiac muscle cell apoptotic process / neutrophil chemotaxis / secretory granule membrane / calcium-mediated signaling / G protein-coupled receptor activity / response to molecule of bacterial origin / receptor internalization / mitotic spindle / positive regulation of angiogenesis / chemotaxis / microtubule cytoskeleton / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / 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 motif chemokine 2 / C-X-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 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 15, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,5103
Polymers62,5103
Non-polymers00
Water00
1


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

-
Components

#1: 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
#2: Protein C-X-C motif chemokine 2


Mass: 7905.440 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19875
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1C-X-C chemokine receptor type 2 in complex with C-X-C motif chemokine 2COMPLEXall0RECOMBINANT
2C-X-C chemokine receptor type 2COMPLEX#11RECOMBINANT
3C-X-C motif chemokine 2COMPLEX#21RECOMBINANT
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
32Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 50.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)
Image scansMovie frames/image: 40

-
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: 1927680
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285884 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: SwissModel / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033420
ELECTRON MICROSCOPYf_angle_d0.4744636
ELECTRON MICROSCOPYf_dihedral_angle_d3.397454
ELECTRON MICROSCOPYf_chiral_restr0.038569
ELECTRON MICROSCOPYf_plane_restr0.003561

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more