+Open data
-Basic information
Entry | Database: PDB / ID: 6be1 | ||||||||||||
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Title | Cryo-EM structure of serotonin receptor | ||||||||||||
Components | 5-hydroxytryptamine receptor 3A | ||||||||||||
Keywords | MEMBRANE PROTEIN / Ion Channel | ||||||||||||
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 | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.31 Å | ||||||||||||
Authors | Basak, S. / Chakrapani, S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Cryo-EM structure of 5-HT receptor in its resting conformation. Authors: Sandip Basak / Yvonne Gicheru / Amrita Samanta / Sudheer Kumar Molugu / Wei Huang / Maria la de Fuente / Taylor Hughes / Derek J Taylor / Marvin T Nieman / Vera Moiseenkova-Bell / Sudha Chakrapani / Abstract: Serotonin receptors (5-HTR) directly regulate gut movement, and drugs that inhibit 5-HTR function are used to control emetic reflexes associated with gastrointestinal pathologies and cancer therapies. ...Serotonin receptors (5-HTR) directly regulate gut movement, and drugs that inhibit 5-HTR function are used to control emetic reflexes associated with gastrointestinal pathologies and cancer therapies. The 5-HTR function involves a finely tuned orchestration of three domain movements that include the ligand-binding domain, the pore domain, and the intracellular domain. Here, we present the structure from the full-length 5-HTR channel in the apo-state determined by single-particle cryo-electron microscopy at a nominal resolution of 4.3 Å. In this conformation, the ligand-binding domain adopts a conformation reminiscent of the unliganded state with the pore domain captured in a closed conformation. In comparison to the 5-HTR crystal structure, the full-length channel in the apo-conformation adopts a more expanded conformation of all the three domains with a characteristic twist that is implicated in gating. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6be1.cif.gz | 544.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6be1.ent.gz | 433.4 KB | Display | PDB format |
PDBx/mmJSON format | 6be1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/6be1 ftp://data.pdbj.org/pub/pdb/validation_reports/be/6be1 | HTTPS FTP |
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-Related structure data
Related structure data | 7088MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 52739.852 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Htr3a / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: E9QLC0, UniProt: P23979*PLUS |
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-Sugars , 6 types, 18 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / #10: Sugar | ChemComp-BMA / | |
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-Non-polymers , 4 types, 18 molecules
#7: Chemical | ChemComp-NA / | ||||
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#8: Chemical | ChemComp-PX4 / #9: Chemical | ChemComp-CL / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Serotonin receptor5-HT receptor / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 270 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Strain: sf9 |
Buffer solution | pH: 8 |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 2.5 sec. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3550 |
Image scans | Movie frames/image: 40 / Used frames/image: 2-39 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 327329 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108727 / Num. of class averages: 2 / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 238 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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