5X2M

Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.206 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for perception of diverse chemical substances by T1r taste receptors

Nuemket, N.Yasui, N.Kusakabe, Y.Nomura, Y.Atsumi, N.Akiyama, S.Nango, E.Kato, Y.Kaneko, M.K.Takagi, J.Hosotani, M.Yamashita, A.

(2017) Nat Commun 8: 15530-15530

  • DOI: 10.1038/ncomms15530
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The taste receptor type 1 (T1r) family perceives 'palatable' tastes. These receptors function as T1r2-T1r3 and T1r1-T1r3 heterodimers to recognize a wide array of sweet and umami (savory) tastes in sugars and amino acids. Nonetheless, it is unclear h ...

    The taste receptor type 1 (T1r) family perceives 'palatable' tastes. These receptors function as T1r2-T1r3 and T1r1-T1r3 heterodimers to recognize a wide array of sweet and umami (savory) tastes in sugars and amino acids. Nonetheless, it is unclear how diverse tastes are recognized by so few receptors. Here we present crystal structures of the extracellular ligand-binding domains (LBDs), the taste recognition regions of the fish T1r2-T1r3 heterodimer, bound to different amino acids. The ligand-binding pocket in T1r2LBD is rich in aromatic residues, spacious and accommodates hydrated percepts. Biophysical studies show that this binding site is characterized by a broad yet discriminating chemical recognition, contributing for the particular trait of taste perception. In contrast, the analogous pocket in T1r3LBD is occupied by a rather loosely bound amino acid, suggesting that the T1r3 has an auxiliary role. Overall, we provide a structural basis for understanding the chemical perception of taste receptors.


    Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Okayama 700-8530, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Taste receptor, type 1, member 2a
A, C
461Oryzias latipesMutation(s): 0 
Gene Names: TAS1R2a
Find proteins for A0A173M0G2 (Oryzias latipes)
Go to UniProtKB:  A0A173M0G2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Taste receptor, type 1, member 3
B, D
478Oryzias latipesMutation(s): 0 
Gene Names: TAS1R3
Find proteins for A0A173M094 (Oryzias latipes)
Go to Gene View: TAS1R3
Go to UniProtKB:  A0A173M094
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab16A Heavy chain
H, J
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab16A Light chain
L, K
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GLN
Query on GLN

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Download CCD File 
A, B, C, D
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.206 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 99.656α = 90.00
b = 116.355β = 92.20
c = 129.476γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Database references