2YME

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with granisetron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 ?
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural Basis of Ligand Recognition in 5-Ht3 Receptors.

Kesters, D.Thompson, A.J.Brams, M.Van Elk, R.Spurny, R.Geitmann, M.Villalgordo, J.M.Guskov, A.Helena Danielson, U.Lummis, S.C.R.Smit, A.B.Ulens, C.

(2013) EMBO Rep 14: 49

  • DOI: https://doi.org/10.1038/embor.2012.189
  • Primary Citation of Related Structures:  
    2YMD, 2YME

  • PubMed Abstract: 

    The 5-HT(3) receptor is a pentameric serotonin-gated ion channel, which mediates rapid excitatory neurotransmission and is the target of a therapeutically important class of anti-emetic drugs, such as granisetron. We report crystal structures of a binding protein engineered to recognize the agonist serotonin and the antagonist granisetron with affinities comparable to the 5-HT(3) receptor. In the serotonin-bound structure, we observe hydrophilic interactions with loop E-binding site residues, which might enable transitions to channel opening. In the granisetron-bound structure, we observe a critical cation-¦Ð interaction between the indazole moiety of the ligand and a cationic centre in loop D, which is uniquely present in the 5-HT(3) receptor. We use a series of chemically tuned granisetron analogues to demonstrate the energetic contribution of this electrostatic interaction to high-affinity ligand binding in the human 5-HT(3) receptor. Our study offers the first structural perspective on recognition of serotonin and antagonism by anti-emetics in the 5-HT(3) receptor.


  • Organizational Affiliation

    Laboratory of Structural Neurobiology, KULeuven, Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
205Aplysia californicaMutation(s): 1 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CWB
Query on CWB

Download Ideal Coordinates CCD File 
CA [auth H]
FA [auth I]
IA [auth J]
L [auth A]
O [auth B]
CA [auth H],
FA [auth I],
IA [auth J],
L [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
Y [auth F],
Z [auth G]
1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide
C18 H24 N4 O
MFWNKCLOYSRHCJ-BTTYYORXSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth H]
EA [auth I]
HA [auth J]
K [auth A]
N [auth B]
BA [auth H],
EA [auth I],
HA [auth J],
K [auth A],
N [auth B],
P [auth C],
T [auth D],
W [auth E],
X [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth G],
DA [auth H],
M [auth A],
R [auth C],
V [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth I]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CWB PDBBind:  2YME Kd: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 ?
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 83.09¦Á = 90
b = 138.9¦Â = 91.07
c = 119.89¦Ã = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Structure summary
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