+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16385 | |||||||||
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Title | Tetrameric 5-HT3aR in Salipro (apo state, symmetric) | |||||||||
Map data | unfiltered EM MAP | |||||||||
Sample |
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Keywords | 5-HT3R / Serotonin / receptor / tetramer / ion channel / MEMBRANE PROTEIN | |||||||||
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 / excitatory extracellular ligand-gated monoatomic ion channel activity / serotonin binding / inorganic cation transmembrane transport / cleavage furrow / transmembrane transporter complex / 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 / excitatory extracellular ligand-gated monoatomic ion channel activity / serotonin binding / inorganic cation transmembrane transport / cleavage furrow / transmembrane transporter complex / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / presynaptic membrane / postsynaptic membrane / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Introini B / Kudryashev M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16385.map.gz | 67.1 MB | EMDB map data format | |
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Header (meta data) | emd-16385-v30.xml emd-16385.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16385_fsc.xml | 15.1 KB | Display | FSC data file |
Images | emd_16385.png | 39.3 KB | ||
Masks | emd_16385_msk_1.map | 137.1 MB | Mask map | |
Filedesc metadata | emd-16385.cif.gz | 5.9 KB | ||
Others | emd_16385_additional_1.map.gz emd_16385_half_map_1.map.gz emd_16385_half_map_2.map.gz | 129.2 MB 127.1 MB 127.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16385 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16385 | HTTPS FTP |
-Validation report
Summary document | emd_16385_validation.pdf.gz | 853 KB | Display | EMDB validaton report |
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Full document | emd_16385_full_validation.pdf.gz | 852.6 KB | Display | |
Data in XML | emd_16385_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_16385_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16385 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16385 | HTTPS FTP |
-Related structure data
Related structure data | 8c1zMC 8c1wC 8c20C 8c21C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16385.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | unfiltered EM MAP | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16385_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: SHARP MAP used for refinement
File | emd_16385_additional_1.map | ||||||||||||
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Annotation | SHARP_MAP used for refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered HALF MAP-A
File | emd_16385_half_map_1.map | ||||||||||||
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Annotation | unfiltered HALF_MAP-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered HALF MAP-B
File | emd_16385_half_map_2.map | ||||||||||||
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Annotation | unfiltered HALF_MAP-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tetrameric 5-HT3A receptor in Salipro (apo, symmetric)
Entire | Name: Tetrameric 5-HT3A receptor in Salipro (apo, symmetric) |
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Components |
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-Supramolecule #1: Tetrameric 5-HT3A receptor in Salipro (apo, symmetric)
Supramolecule | Name: Tetrameric 5-HT3A receptor in Salipro (apo, symmetric) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: 5-hydroxytryptamine receptor 3A
Macromolecule | Name: 5-hydroxytryptamine receptor 3A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 60.668086 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQGATQA RDTTQPALL RLSDHLLANY KKGVRPVRDW RKPTTVSIDV IMYAILNVDE KNQVLTTYIW YRQYWTDEFL QWTPEDFDNV T KLSIPTDS ...String: MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQGATQA RDTTQPALL RLSDHLLANY KKGVRPVRDW RKPTTVSIDV IMYAILNVDE KNQVLTTYIW YRQYWTDEFL QWTPEDFDNV T KLSIPTDS IWVPDILINE FVDVGKSPNI PYVYVHHRGE VQNYKPLQLV TACSLDIYNF PFDVQNCSLT FTSWLHTIQD IN ITLWRSP EEVRSDKSIF INQGEWELLE VFPQFKEFSI DISNSYAEMK FYVIIRRRPL FYAVSLLLPS IFLMVVDIVG FCL PPDSGE RVSFKITLLL GYSVFLIIVS DTLPATAIGT PLIGVYFVVC MALLVISLAE TIFIVRLVHK QDLQRPVPDW LRHL VLDRI AWILCLGEQP MAHRPPATFQ ANKTDDCSGS DLLPAMGNHC SHVGGPQDLE KTPRGRGSPL PPPREASLAV RGLLQ ELSS IRHFLEKRDE MREVARDWLR VGYVLDRLLF RIYLLAVLAY SITLVTLWSI WHSS UniProtKB: 5-hydroxytryptamine receptor 3A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |