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- EMDB-7882: Full-length 5-HT3A receptor in a serotonin-bound conformation- State 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-7882
TitleFull-length 5-HT3A receptor in a serotonin-bound conformation- State 1
Map dataserotonin bound 5HT3A receptor (state 1)
Sample
  • Organelle or cellular component: Serotonin receptor5-HT receptor
    • Protein or peptide: 5-hydroxytryptamine receptor 3A
  • Ligand: SEROTONIN
  • Ligand: water
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / serotonin binding / acetylcholine-gated monoatomic cation-selective channel activity / inorganic cation transmembrane transport / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic membrane ...Neurotransmitter receptors and postsynaptic signal transmission / serotonin-gated monoatomic cation channel activity / serotonin-activated cation-selective channel complex / serotonin receptor signaling pathway / serotonin binding / acetylcholine-gated monoatomic cation-selective channel activity / inorganic cation transmembrane transport / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic membrane / postsynaptic membrane / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / identical protein binding
Similarity search - Function
5-hydroxytryptamine 3 receptor / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain ...5-hydroxytryptamine 3 receptor / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
5-hydroxytryptamine receptor 3A / 5-hydroxytryptamine receptor 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsBasak S / Chakrapani S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM108921 United States
American Heart Association17POST33671152 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM108921-03S1 United States
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 /
Abstract: The 5-HT serotonin receptor, a cationic pentameric ligand-gated ion channel (pLGIC), is the clinical target for management of nausea and vomiting associated with radiation and chemotherapies. Upon ...The 5-HT serotonin receptor, a cationic pentameric ligand-gated ion channel (pLGIC), is the clinical target for management of nausea and vomiting associated with radiation and chemotherapies. Upon binding, serotonin induces a global conformational change that encompasses the ligand-binding extracellular domain (ECD), the transmembrane domain (TMD) and the intracellular domain (ICD), the molecular details of which are unclear. Here we present two serotonin-bound structures of the full-length 5-HT receptor in distinct conformations at 3.32 Å and 3.89 Å resolution that reveal the mechanism underlying channel activation. In comparison to the apo 5-HT receptor, serotonin-bound states underwent a large twisting motion in the ECD and TMD, leading to the opening of a 165 Å permeation pathway. Notably, this motion results in the creation of lateral portals for ion permeation at the interface of the TMD and ICD. Combined with molecular dynamics simulations, these structures provide novel insights into conformational coupling across domains and functional modulation.
History
DepositionMay 17, 2018-
Header (metadata) releaseMay 30, 2018-
Map releaseNov 7, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dg7
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7882.png

Downloads & links

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Map

FileDownload / File: emd_7882.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationserotonin bound 5HT3A receptor (state 1)
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.040867012 - 0.13483115
Average (Standard dev.)0.0005499486 (±0.0040724366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 319.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z319.200319.200319.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0410.1350.001

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Supplemental data

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Mask #1

Fileemd_7882_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: serotonin bound 5HT3A receptor (state 1), half map #1

Fileemd_7882_half_map_1.map
Annotationserotonin bound 5HT3A receptor (state 1), half map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: serotonin bound 5HT3A receptor (state 1), half map #2

Fileemd_7882_half_map_2.map
Annotationserotonin bound 5HT3A receptor (state 1), half map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Serotonin receptor

EntireName: Serotonin receptor5-HT receptor
Components
  • Organelle or cellular component: Serotonin receptor5-HT receptor
    • Protein or peptide: 5-hydroxytryptamine receptor 3A
  • Ligand: SEROTONIN
  • Ligand: water

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Supramolecule #1: Serotonin receptor

SupramoleculeName: Serotonin receptor / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 270 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: sf9

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Macromolecule #1: 5-hydroxytryptamine receptor 3A

MacromoleculeName: 5-hydroxytryptamine receptor 3A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 52.52366 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TQPALLRLSD HLLANYKKGV RPVRDWRKPT TVSIDVIMYA ILNVDEKNQV LTTYIWYRQY WTDEFLQWTP EDFDNVTKLS IPTDSIWVP DILINEFVDV GKSPNIPYVY VHHRGEVQNY KPLQLVTACS LDIYNFPFDV QNCSLTFTSW LHTIQDINIT L WRSPEEVR ...String:
TQPALLRLSD HLLANYKKGV RPVRDWRKPT TVSIDVIMYA ILNVDEKNQV LTTYIWYRQY WTDEFLQWTP EDFDNVTKLS IPTDSIWVP DILINEFVDV GKSPNIPYVY VHHRGEVQNY KPLQLVTACS LDIYNFPFDV QNCSLTFTSW LHTIQDINIT L WRSPEEVR SDKSIFINQG EWELLEVFPQ FKEFSIDISN SYAEMKFYVI IRRRPLFYAV SLLLPSIFLM VVDIVGFCLP PD SGERVSF KITLLLGYSV FLIIVSDTLP ATAIGTPLIG VYFVVCMALL VISLAETIFI VRLVHKQDLQ RPVPDWLRHL VLD RIAWIL CLGEQPMAHR PPATFQANKT DDCSGSDLLP AMGNHCSHVG GPQDLEKTPR GRGSPLPPPR EASLAVRGLL QELS SIRHF LEKRDEMREV ARDWLRVGYV LDRLLFRIYL LAVLAYSITL VTLWSIWHYS

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Macromolecule #4: SEROTONIN

MacromoleculeName: SEROTONIN / type: ligand / ID: 4 / Number of copies: 5 / Formula: SRO
Molecular weightTheoretical: 176.215 Da
Chemical component information

ChemComp-SRO:
SEROTONIN / neurotransmitter*YM / Serotonin

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I / Details: blot for 2.5 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-39 / Number real images: 2810 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 749970
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6be1

Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 103698

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 154
Output model

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

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