2YME | pdb_00002yme

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

PDB DOI: https://doi.org/10.2210/pdb2YME/pdb

Classification: RECEPTOR
Organism(s): Aplysia californica
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2012-10-09 Released: 2012-12-26
Deposition Author(s): Kesters, D., Thompson, A.J., Brams, M., Elk, R.v., Spurny, R., Geitmann, M., Villalgordo, J.M., Guskov, A., Danielson, U.H., Lummis, S.C.R., Smit, A.B., Ulens, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.226 (Depositor), 0.221 (DCC)
R-Value Work:
0.170 (Depositor), 0.168 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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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

PubMed: 23196367 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/embor.2012.189
Primary Citation 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-π 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.

Macromolecule Content

Total Structure Weight: 239.04 kDa
Atom Count: 18,055
Modeled Residue Count: 2,050
Deposited Residue Count: 2,050
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SOLUBLE ACETYLCHOLINE RECEPTOR	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	205	Aplysia californica	Mutation(s): 1
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8 Go to UniProtKB: Q8WSF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WSF8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CWB Query on CWB Download:Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain FA [auth I] SDF format, chain IA [auth J] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain Y [auth F] SDF format, chain Z [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain FA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain FA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth G]	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		Interactions Focus chain CA [auth H] Focus chain FA [auth I] Focus chain IA [auth J] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain CA [auth H] Focus chain FA [auth I] Focus chain IA [auth J] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain Y [auth F] Focus chain Z [auth G]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain EA [auth I] SDF format, chain HA [auth J] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain X [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain EA [auth I] mmCIF format, chain HA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth F]	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		Interactions Focus chain BA [auth H] Focus chain EA [auth I] Focus chain HA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth F] Interactions & Density Focus chain BA [auth H] Focus chain EA [auth I] Focus chain HA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain M [auth A] SDF format, chain R [auth C] SDF format, chain V [auth E] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain R [auth C] MOL2 format, chain V [auth E] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain R [auth C] mmCIF format, chain V [auth E]	AA [auth G], DA [auth H], M [auth A], R [auth C], V [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain M [auth A] Focus chain R [auth C] Focus chain V [auth E] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain M [auth A] Focus chain R [auth C] Focus chain V [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain GA [auth I] MOL2 format, chain GA [auth I] mmCIF format, chain GA [auth I]	GA [auth I]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain GA [auth I] Interactions & Density Focus chain GA [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.226 (Depositor), 0.221 (DCC)
R-Value Work: 0.170 (Depositor), 0.168 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.09	α = 90
b = 138.9	β = 91.07
c = 119.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-12-26

Deposition Author(s):

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