6IBB

Crystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91) in complex with a nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of species-selective antagonist binding to the succinate receptor.

Haffke, M.Fehlmann, D.Rummel, G.Boivineau, J.Duckely, M.Gommermann, N.Cotesta, S.Sirockin, F.Freuler, F.Littlewood-Evans, A.Kaupmann, K.Jaakola, V.P.

(2019) Nature 574: 581-585

  • DOI: 10.1038/s41586-019-1663-8
  • Primary Citation of Related Structures:  
    6IBB, 6RNK

  • PubMed Abstract: 
  • The tricarboxylic acid cycle intermediate succinate is involved in metabolic processes and plays a crucial role in the homeostasis of mitochondrial reactive oxygen species 1 . The receptor responsible for succinate signalling, SUCNR1 (also known as GPR91), is a member of the G-protein-coupled-receptor family 2 and links succinate signalling to renin-induced hypertension, retinal angiogenesis and inflammation 3-5 ...

    The tricarboxylic acid cycle intermediate succinate is involved in metabolic processes and plays a crucial role in the homeostasis of mitochondrial reactive oxygen species 1 . The receptor responsible for succinate signalling, SUCNR1 (also known as GPR91), is a member of the G-protein-coupled-receptor family 2 and links succinate signalling to renin-induced hypertension, retinal angiogenesis and inflammation 3-5 . Because SUCNR1 senses succinate as an immunological danger signal 6 -which has relevance for diseases including ulcerative colitis, liver fibrosis 7 , diabetes and rheumatoid arthritis 3,8 -it is of interest as a therapeutic target. Here we report the high-resolution crystal structure of rat SUCNR1 in complex with an intracellular binding nanobody in the inactive conformation. Structure-based mutagenesis and radioligand-binding studies, in conjunction with molecular modelling, identified key residues for species-selective antagonist binding and enabled the determination of the high-resolution crystal structure of a humanized rat SUCNR1 in complex with a high-affinity, human-selective antagonist denoted NF-56-EJ40. We anticipate that these structural insights into the architecture of the succinate receptor and its antagonist selectivity will enable structure-based drug discovery and will further help to elucidate the function of SUCNR1 in vitro and in vivo.


    Organizational Affiliation

    Confo Therapeutics, Zwijnaarde, Belgium. veli-pekka.jaakola@confotherapeutics.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate receptor 1A, C342Rattus norvegicusMutation(s): 0 
Gene Names: Sucnr1Gpr91
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
succinate receptor SUCNR1 (GPR91)
Find proteins for Q6IYF9 (Rattus norvegicus)
Explore Q6IYF9 
Go to UniProtKB:  Q6IYF9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody6B, D142Vicugna pacosMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
Q [auth C]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
OLC
Query on OLC

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  O [auth C],  P [auth C],  R [auth C],  S [auth C],  T [auth C],  U [auth C],  V [auth C]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
H95
Query on H95

Download Ideal Coordinates CCD File 
N [auth A](2~{S},5~{R})-hexane-2,5-diol
C6 H14 O2
OHMBHFSEKCCCBW-OLQVQODUSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A], W [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.22α = 90
b = 164β = 102.63
c = 63.42γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references