6HIO

Mouse serotonin 5-HT3 receptor, serotonin-bound, I1 conformation

PDB DOI: https://doi.org/10.2210/pdb6HIO/pdb
EM Map EMD-0226: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2018-08-30 Released: 2018-11-07
Deposition Author(s): Polovinkin, L., Neumann, E., Schoehn, G., Nury, H.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 266.76 kDa
Atom Count: 16,085
Modelled Residue Count: 1,925
Deposited Residue Count: 2,260
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 3A	A, B [auth E], C [auth B], D [auth C], E [auth D]	452	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23979
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain P [auth A] MOL2 format, chain S [auth E] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain P [auth A]	P [auth A], S [auth E], T [auth B], V [auth C], Y [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Focus chain S [auth E] Focus chain T [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain P [auth A] Focus chain S [auth E] Focus chain T [auth B] Focus chain V [auth C] Focus chain Y [auth D]
SRO Query on SRO Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth E] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain X [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth E] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D]	Q [auth A], R [auth E], U [auth B], W [auth C], X [auth D]	SEROTONIN C₁₀ H₁₂ N₂ O QZAYGJVTTNCVMB-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth E] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth D] Interactions & Density Focus chain Q [auth A] Focus chain R [auth E] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
SRO	BindingDB: 6HIO	Ki: min: 66, max: 1.00e+4 (nM) from 10 assay(s)
		IC50: 727 (nM) from 1 assay(s)
		EC50: min: 141, max: 1.20e+4 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-07
Type: Initial release
Version 1.1: 2018-11-21
Changes: Data collection, Database references
Version 1.2: 2019-04-03
Changes: Data collection, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2022-09-14
Changes: Atomic model, Data collection, Database references, Source and taxonomy, Structure summary

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Deposit Data

Help and Resources

6HIO

Mouse serotonin 5-HT3 receptor, serotonin-bound, I1 conformation

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)