6Y1Z

Mouse serotonin 5HT3 receptor in complex with palonosetron

• PDB DOI: https://doi.org/10.2210/pdb6Y1Z/pdb
• EM Map EMD-10673: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-02-14 Released: 2020-03-04 
• Deposition Author(s): Zarkadas, E., Perot, J., Nury, H.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 327.86 kDa 
• Atom Count: 16,610 
• Modelled Residue Count: 1,920 
• Deposited Residue Count: 2,830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 3A	A, B [auth D], C [auth B], D [auth C], E	566	Mus musculus	Mutation(s): 0  Gene Names: Htr3a, 5ht3, Htr3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23979 (Mus musculus) Explore P23979  Go to UniProtKB:  P23979
IMPC:  MGI:96282

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, J, L, N	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K, M, O	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O7B (Subject of Investigation/LOI)	AA [auth B], BA [auth C], FA [auth E], S [auth A], W [auth D]	(3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one C19 H24 N2 O CPZBLNMUGSZIPR-NVXWUHKLSA-N
NAG	EA [auth C], IA [auth E], R [auth A], V [auth D], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRP	CA [auth C], GA [auth E], P [auth A], T [auth D], X [auth B]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
HIS	DA [auth C], HA [auth E], Q [auth A], U [auth D], Y [auth B]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
O7B	BindingDB:  6Y1Z	Ki: min: 0.03, max: 0.04 (nM) from 2 assay(s)
		Kd: min: 0.18, max: 0.32 (nM) from 2 assay(s)
		IC50: min: 0.83, max: 0.88 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v2.13
MODEL REFINEMENT	PHENIX	1.17

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Zarkadas, E., Perot, J., Nury, H.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	France	637733

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-08-12
  Changes: Database references, Structure summary
• Version 2.2: 2020-10-14
  Changes: Database references
• Version 3.0: 2022-09-14
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary