[English] 日本語
Yorodumi- EMDB-13816: CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tund... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13816 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope | |||||||||
Map data | CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope | |||||||||
Sample |
| |||||||||
Keywords | Ion channel / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / neurotransmitter receptor activity ...cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / neurotransmitter receptor activity / roof of mouth development / Signaling by ERBB4 / chloride channel complex / transmembrane transporter complex / chloride transmembrane transport / cytoplasmic vesicle membrane / neuron projection / synapse / signal transduction / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | HEK 293S cells (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Karia D / Koh AF / Yu L / Kotecha A | |||||||||
Funding support | Netherlands, 1 items
| |||||||||
Citation | Journal: To Be Published Title: CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope Authors: Karia D / Koh AF / Yu L / Kotecha A | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13816.map.gz | 4.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-13816-v30.xml emd-13816.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13816_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_13816.png | 157.9 KB | ||
Filedesc metadata | emd-13816.cif.gz | 3.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13816 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13816 | HTTPS FTP |
-Validation report
Summary document | emd_13816_validation.pdf.gz | 379.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_13816_full_validation.pdf.gz | 378.8 KB | Display | |
Data in XML | emd_13816_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_13816_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13816 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13816 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
EM raw data | EMPIAR-10858 (Title: CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope Data size: 2.2 TB Data #1: Unaligned multiframe movies of GABAA receptor from CETA-F camera [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_13816.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.50242 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human GABA(A)R-beta3 homopentamer
Entire | Name: Human GABA(A)R-beta3 homopentamer |
---|---|
Components |
|
-Supramolecule #1: Human GABA(A)R-beta3 homopentamer
Supramolecule | Name: Human GABA(A)R-beta3 homopentamer / type: complex / ID: 1 / Parent: 0 Details: Human GABA(A)R-beta3 homopentamer in complex with Megabody-25 in lipid nanodisc |
---|---|
Source (natural) | Organism: HEK 293S cells (E. coli) |
Molecular weight | Theoretical: 200 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
---|---|
Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 287 K / Instrument: LEICA PLUNGER |
-Electron microscopy
Microscope | TFS TUNDRA |
---|---|
Image recording | Film or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3952 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal magnification: 180000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |