6RNK

Crystal structure of a humanized (K18E, K269N) rat succinate receptor SUCNR1 (GPR91) in complex with a nanobody and antagonist NF-56-EJ40.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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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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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate receptor 1A342Rattus norvegicusMutation(s): 2 
Gene Names: Sucnr1, Gpr91
Membrane Entity: Yes 
UniProt
Find proteins for Q6IYF9 (Rattus norvegicus)
Explore Q6IYF9 
Go to UniProtKB:  Q6IYF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IYF9
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody6B142Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAZ
Query on KAZ
Download Ideal Coordinates CCD File 
C [auth A]2-[2-[[3-[4-[(4-methylpiperazin-1-yl)methyl]phenyl]phenyl]carbonylamino]phenyl]ethanoic acid
C27 H29 N3 O3
UTWXDNZWMQAUKL-UHFFFAOYSA-N		 Ligand Interaction
OLC
Query on OLC
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
D [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],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
R [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
Q [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.83α = 90
b = 150.93β = 112.42
c = 68.23γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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