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 1.3 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 30: 1016

  • DOI: https://doi.org/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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 183A [auth R]384Homo sapiensMutation(s): 0 
Gene Names: GPR183EBI2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P32249 (Homo sapiens)
Explore P32249 
Go to UniProtKB:  P32249
PHAROS:  P32249
GTEx:  ENSG00000169508 
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UniProt GroupP32249
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]356Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence 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 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16266Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Binding Affinity Annotations 
IDSourceBinding Affinity
KJX BindingDB:  7TUZ EC50: min: 0.03, max: 1.3 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary