2YMD | pdb_00002ymd

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

PDB DOI: https://doi.org/10.2210/pdb2YMD/pdb

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

Deposited: 2012-10-09 Released: 2012-12-12
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: 1.96 Å
R-Value Free:
0.201 (Depositor), 0.199 (DCC)
R-Value Work:
0.159 (Depositor), 0.164 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Basis of Ligand Recognition in 5-Ht(3) 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., 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: 244.93 kDa
Atom Count: 19,801
Modeled Residue Count: 2,111
Deposited Residue Count: 2,120
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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	212	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRO Query on SRO Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth H] SDF format, chain NA [auth I] SDF format, chain O [auth B] SDF format, chain PA [auth J] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain IA [auth G] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain NA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain IA [auth G] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain NA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain IA [auth G]	AA [auth E] EA [auth F] IA [auth G] K [auth A] LA [auth H] AA [auth E], EA [auth F], IA [auth G], K [auth A], LA [auth H], NA [auth I], O [auth B], PA [auth J], S [auth C], W [auth D]	SEROTONIN C₁₀ H₁₂ N₂ O QZAYGJVTTNCVMB-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain O [auth B] Focus chain PA [auth J] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain O [auth B] Focus chain PA [auth J] Focus chain S [auth C] Focus chain W [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth H] SDF format, chain OA [auth I] SDF format, chain Q [auth B] SDF format, chain QA [auth J] SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain JA [auth G] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain OA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain JA [auth G] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain OA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain JA [auth G]	CA [auth E] GA [auth F] JA [auth G] M [auth A] MA [auth H] CA [auth E], GA [auth F], JA [auth G], M [auth A], MA [auth H], OA [auth I], Q [auth B], QA [auth J], U [auth C], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain U [auth C] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain HA [auth F] SDF format, chain KA [auth G] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain V [auth D] SDF format, chain RA [auth J] SDF format, chain P [auth B] SDF format, chain DA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain V [auth D] MOL2 format, chain RA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain DA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain KA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain V [auth D] mmCIF format, chain RA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain DA [auth F]	BA [auth E] DA [auth F] FA [auth F] HA [auth F] KA [auth G] BA [auth E], DA [auth F], FA [auth F], HA [auth F], KA [auth G], L [auth A], N [auth B], P [auth B], R [auth B], RA [auth J], T [auth C], V [auth D], X [auth D], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain DA [auth F] Focus chain FA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain RA [auth J] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain DA [auth F] Focus chain FA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain RA [auth J] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.201 (Depositor), 0.199 (DCC)
R-Value Work: 0.159 (Depositor), 0.164 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.565	α = 90
b = 140.064	β = 99.08
c = 126.528	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2013-01-30
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary