7TUZ

Cryo-EM structure of 7alpha,25-dihydroxycholesterol-bound EBI2/GPR183 in complex with Gi protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 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

Structures of oxysterol sensor EBI2/GPR183, a key regulator of the immune response.

Chen, H.Huang, W.Li, X.

(2022) Structure 

  • DOI: 10.1016/j.str.2022.04.006
  • Primary Citation of Related Structures:  
    7TUY, 7TUZ

  • PubMed Abstract: 
  • Oxysterols induce the migration of B-lymphocytes and dendritic cells to interfollicular regions of lymphoid tissues through binding the EBI2 (GPR183) to stimulate effective adaptive immunity and antibody production during infection. Aberrant EBI2 signaling is implicated in inflammatory bowel disease, sclerosis, and infectious disease ...

    Oxysterols induce the migration of B-lymphocytes and dendritic cells to interfollicular regions of lymphoid tissues through binding the EBI2 (GPR183) to stimulate effective adaptive immunity and antibody production during infection. Aberrant EBI2 signaling is implicated in inflammatory bowel disease, sclerosis, and infectious disease. Here, we report the cryo-EM structures of an EBI2-G i signaling complex with its endogenous agonist 7α,25-OHC and that of an inactive EBI2 bound to the inverse agonist GSK682753A. These structures reveal an agonist binding site for the oxysterol and a potential ligand entrance site exposed to the lipid bilayer. Mutations within the oxysterol binding site and the Gα i interface attenuate G protein signaling and abolish oxysterol-mediated cell migration indicating that G protein signaling directly involves in the oxysterol-EBI2 pathway. Together, these findings provide new insight into how EBI2 is activated by an oxysterol ligand and will facilitate the development of therapeutic approaches that target EBI2-linked diseases.


    Organizational Affiliation

    Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: xiaochun.li@utsouthwestern.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
G-protein coupled receptor 183A [auth R]384Homo sapiensMutation(s): 0 
Gene Names: GPR183EBI2
Membrane Entity: Yes 
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Find proteins for P32249 (Homo sapiens)
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PHAROS:  P32249
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UniProt GroupP32249
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]356Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
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UniProt GroupP62873
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth C]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
scFv16E266Mus musculusMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KJX (Subject of Investigation/LOI)
Query on KJX

Download Ideal Coordinates CCD File 
F [auth R](2S,4aS,4bS,7R,8S,8aS,9R,10aR)-7-[(2R,3R)-7-hydroxy-3,7-dimethyloctan-2-yl]-4a,7,8-trimethyltetradecahydrophenanthrene-2,9-diol
C27 H46 O3
BQMSKLCEWBSPPY-IKVTXIKFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01HL020948
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM135343
Damon Runyon Cancer Research FoundationUnited StatesDRR-53S-19

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references