+Open data
-Basic information
Entry | Database: PDB / ID: 8c1w | ||||||
---|---|---|---|---|---|---|---|
Title | Tetrameric 5-HT3A receptor in Salipro (apo, asymmetric) | ||||||
Components | 5-hydroxytryptamine receptor 3A | ||||||
Keywords | MEMBRANE PROTEIN / 5-HT3R / Serotonin / receptor / tetramer | ||||||
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 / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 / serotonin binding / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Introini, B. / Kudryashev, M. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: To Be Published Title: Tetrameric structure of the serotonin receptor ion channel 5-HT3A Authors: Introini, B. / Cui, W. / Eckhardt-Sterlau, L. / Tol, M. / Vogel, H. / Yuan, S. / Kudryashev, M. #1: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8c1w.cif.gz | 278 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8c1w.ent.gz | 219.9 KB | Display | PDB format |
PDBx/mmJSON format | 8c1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c1w_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8c1w_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8c1w_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 8c1w_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/8c1w ftp://data.pdbj.org/pub/pdb/validation_reports/c1/8c1w | HTTPS FTP |
-Related structure data
Related structure data | 16384MC 8c1zC 8c20C 8c21C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 60668.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Htr3a, 5ht3, Htr3 / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P23979 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetrameric 5-HT3aR receptor in Salipro (apo, asymmetric) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.220 MDa / Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: HEK |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 384937 / Symmetry type: POINT |