6LFO

Cryo-EM structure of a class A GPCR monomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of CXC chemokine receptor 2 activation and signalling.

Liu, K.Wu, L.Yuan, S.Wu, M.Xu, Y.Sun, Q.Li, S.Zhao, S.Hua, T.Liu, Z.J.

(2020) Nature 585: 135-140

  • DOI: https://doi.org/10.1038/s41586-020-2492-5
  • Primary Citation of Related Structures:  
    6LFL, 6LFM, 6LFO

  • PubMed Abstract: 

    Chemokines and their receptors mediate cell migration, which influences multiple fundamental biological processes and disease conditions such as inflammation and cancer 1 . Although ample effort has been invested into the structural investigation of the chemokine receptors and receptor-chemokine recognition 2-4 , less is known about endogenous chemokine-induced receptor activation and G-protein coupling. Here we present the cryo-electron microscopy structures of interleukin-8 (IL-8, also known as CXCL8)-activated human CXC chemokine receptor 2 (CXCR2) in complex with G i  protein, along with a crystal structure of CXCR2 bound to a designed allosteric antagonist. Our results reveal a unique shallow mode of binding between CXCL8 and CXCR2, and also show the interactions between CXCR2 and G i  protein. Further structural analysis of the inactive and active states of CXCR2 reveals a distinct activation process and the competitive small-molecule antagonism of chemokine receptors. In addition, our results provide insights into how a G-protein-coupled receptor is activated by an endogenous protein molecule, which will assist in the rational development of therapeutics that target the chemokine system for better pharmacological profiles.


  • Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1353Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane Entity: Yes 
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PHAROS:  P63096
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UniProt GroupP63096
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1346Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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PHAROS:  P59768
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-865Homo sapiensMutation(s): 0 
Gene Names: CXCL8IL8
Membrane Entity: Yes 
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Find proteins for P10145 (Homo sapiens)
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PHAROS:  P10145
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UniProt GroupP10145
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
C-X-C chemokine receptor type 2E [auth R]360Homo sapiensMutation(s): 0 
Gene Names: CXCR2IL8RB
Membrane Entity: Yes 
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Find proteins for P25025 (Homo sapiens)
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Go to UniProtKB:  P25025
PHAROS:  P25025
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UniProt GroupP25025
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16F [auth S]259Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.11

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references