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Yorodumi- EMDB-21518: Cryo-EM structure of 5HT3A receptor in presence of Palonosetron -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21518 | |||||||||
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Title | Cryo-EM structure of 5HT3A receptor in presence of Palonosetron | |||||||||
Map data | 5HT3A receptor in presence of Palonosetron | |||||||||
Sample |
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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 / extracellular ligand-gated monoatomic ion channel activity / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...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 / extracellular ligand-gated monoatomic ion channel activity / cleavage furrow / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmembrane signaling receptor activity / 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 | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Basak S / Chakrapani S | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Molecular mechanism of setron-mediated inhibition of full-length 5-HT receptor. Authors: Sandip Basak / Yvonne Gicheru / Abhijeet Kapoor / Megan L Mayer / Marta Filizola / Sudha Chakrapani / Abstract: Serotonin receptor (5-HTR) is the most common therapeutic target to manage the nausea and vomiting during cancer therapies and in the treatment of irritable bowel syndrome. Setrons, a class of ...Serotonin receptor (5-HTR) is the most common therapeutic target to manage the nausea and vomiting during cancer therapies and in the treatment of irritable bowel syndrome. Setrons, a class of competitive antagonists, cause functional inhibition of 5-HTR in the gastrointestinal tract and brainstem, acting as effective anti-emetic agents. Despite their prevalent use, the molecular mechanisms underlying setron binding and inhibition of 5-HTR are not fully understood. Here, we present the structure of granisetron-bound full-length 5-HTR solved by single-particle cryo-electron microscopy to 2.92 Å resolution. The reconstruction reveals the orientation of granisetron in the orthosteric site with unambiguous density for interacting sidechains. Molecular dynamics simulations and electrophysiology confirm the granisetron binding orientation and the residues central for ligand recognition. Comparison of granisetron-bound 5-HTR with the apo and serotonin-bound structures, reveals key insights into the mechanism underlying 5-HTR inhibition. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21518.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-21518-v30.xml emd-21518.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_21518.png | 276.7 KB | ||
Masks | emd_21518_msk_1.map | 103 MB | Mask map | |
Others | emd_21518_half_map_1.map.gz emd_21518_half_map_2.map.gz | 80.3 MB 80.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21518 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21518 | HTTPS FTP |
-Related structure data
Related structure data | 6w1yMC 6w1jC 6w1mC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21518.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 5HT3A receptor in presence of Palonosetron | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.848 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21518_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_21518_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_21518_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Serotonin receptor
Entire | Name: Serotonin receptor5-HT receptor |
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Components |
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-Supramolecule #1: Serotonin receptor
Supramolecule | Name: Serotonin receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 270 KDa |
-Macromolecule #1: 5-hydroxytryptamine receptor 3A
Macromolecule | Name: 5-hydroxytryptamine receptor 3A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 52.042121 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: TTQPALLRLS DHLLANYKKG VRPVRDWRKP TTVSIDVIMY AILNVDEKNQ VLTTYIWYRQ YWTDEFLQWT PEDFDNVTKL SIPTDSIWV PDILINEFVD VGKSPNIPYV YVHHRGEVQN YKPLQLVTAC SLDIYNFPFD VQNCSLTFTS WLHTIQDINI T LWRSPEEV ...String: TTQPALLRLS DHLLANYKKG VRPVRDWRKP TTVSIDVIMY AILNVDEKNQ VLTTYIWYRQ YWTDEFLQWT PEDFDNVTKL SIPTDSIWV PDILINEFVD VGKSPNIPYV YVHHRGEVQN YKPLQLVTAC SLDIYNFPFD VQNCSLTFTS WLHTIQDINI T LWRSPEEV RSDKSIFINQ GEWELLEVFP QFKEFSIDIS NSYAEMKFYV IIRRRPLFYA VSLLLPSIFL MVVDIVGFCL PP DSGERVS FKITLLLGYS VFLIIVSDTL PATAIGTPLI GVYFVVCMAL LVISLAETIF IVRLVHKQDL QRPVPDWLRH LVL DRIAWI LCLGEQPMAH RPPATFQANK TDDCSAMGNH CSHVGGPQDL EKTPRGRGSP LPPPREASLA VRGLLQELSS IRHF LEKRD EMREVARDWL RVGYVLDRLL FRIYLLAVLA YSITLVTLWS IWHYS |
-Macromolecule #5: (3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6...
Macromolecule | Name: (3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one type: ligand / ID: 5 / Number of copies: 5 / Formula: O7B |
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Molecular weight | Theoretical: 296.407 Da |
Chemical component information | ChemComp-O7B: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I / Details: blot for 2.5 seconds. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Number real images: 5970 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1114542 |
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CTF correction | Software - Name: Gctf (ver. 1.06) |
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1) |
Final 3D classification | Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 91163 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 70 |
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Output model | PDB-6w1y: |