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- PDB-6dg7: Full-length 5-HT3A receptor in a serotonin-bound conformation- State 1 -

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Basic information

Entry
Database: PDB / ID: 6dg7
TitleFull-length 5-HT3A receptor in a serotonin-bound conformation- State 1
Components5-hydroxytryptamine receptor 3A
KeywordsMEMBRANE PROTEIN
Function / homologyNeurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter receptors and postsynaptic signal transmission / 5-hydroxytryptamine 3 receptor / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain ...Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter receptors and postsynaptic signal transmission / 5-hydroxytryptamine 3 receptor / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / serotonin-activated cation-selective channel complex / serotonin-gated cation-selective channel activity / serotonin binding / positive regulation of ion transmembrane transporter activity / cleavage furrow / response to cocaine / integral component of postsynaptic membrane / integral component of presynaptic membrane / cellular response to growth factor stimulus / transmembrane signaling receptor activity / response to ethanol / glutamatergic synapse / axon / neuronal cell body / cytoplasm / 5-hydroxytryptamine receptor 3A
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.32 Å resolution
AuthorsBasak, S. / Chakrapani, S.
CitationJournal: Nature / Year: 2018
Title: Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT receptor.
Authors: Sandip Basak / Yvonne Gicheru / Shanlin Rao / Mark S P Sansom / Sudha Chakrapani
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 17, 2018 / Release: Nov 7, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 7, 2018Structure modelrepositoryInitial release
1.1Nov 21, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 3A
B: 5-hydroxytryptamine receptor 3A
C: 5-hydroxytryptamine receptor 3A
D: 5-hydroxytryptamine receptor 3A
E: 5-hydroxytryptamine receptor 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,03645
Polyers262,6185
Non-polymers8,41840
Water905
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)41270
ΔGint (kcal/M)-181
Surface area (Å2)101940

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Components

#1: Protein/peptide
5-hydroxytryptamine receptor 3A / Serotonin receptor


Mass: 52523.660 Da / Num. of mol.: 5 / Fragment: UNP residues 35-489 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Htr3a / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: E9QLC0
#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 30 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 5 / Formula: C6H12O6
#4: Chemical
ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 5 / Formula: C10H12N2O / Serotonin
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Serotonin receptor5-HT receptor / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: sf9
Buffer solutionpH: 8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: blot for 2.5 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 / Cs: 2.7 mm / C2 aperture diameter: 70 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 2810
Image scansMovie frames/image: 40 / Used frames/image: 2-39

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
4Gctf1.06CTF correction
7Coot0.8.9model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.13-2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 749970
SymmetryPoint symmetry: C5
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 103698 / Symmetry type: POINT
Atomic model buildingOverall b value: 154 / Ref protocol: OTHER / Ref space: REAL

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