6DG8
Full-length 5-HT3A receptor in a serotonin-bound conformation- State 2
- PDB DOI: https://doi.org/10.2210/pdb6DG8/pdb
- EM Map EMD-7883: EMDB EMDataResource
- Classification: MEMBRANE PROTEIN
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc
- Deposited: 2018-05-17 Released: 2018-11-07 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.89 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
5-hydroxytryptamine receptor 3A | 455 | Mus musculus | Mutation(s): 0  Gene Names: Htr3a 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 AnnotationsExpand | |||||
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Oligosaccharides
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, H, J, K, M F, H, J, K, M, N, P, Q, S, T | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 3 | |||||
---|---|---|---|---|---|
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 | G, I, L, O, R | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SRO Query on SRO | U [auth A], V [auth B], W [auth B], X [auth D], Y [auth E] | SEROTONIN C10 H12 N2 O QZAYGJVTTNCVMB-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.89 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | RELION | 2.1 |
MODEL REFINEMENT | PHENIX | 1.13-2998 |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-11-07  Deposition Author(s): Basak, S., Chakrapani, S.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 1R01GM108921 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 3R01GM108921-03S1 |
American Heart Association | United States | 17POST33671152 |
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: 2020-01-08
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary