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Yorodumi- EMDB-7980: Human type 3 1,4,5-inositol trisphosphate receptor in a ligand-fr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7980 | |||||||||
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Title | Human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state | |||||||||
Map data | Single subunit refinement of human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 Å | |||||||||
Authors | Hite RK / Paknejad N | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Structural basis for the regulation of inositol trisphosphate receptors by Ca and IP. Authors: Navid Paknejad / Richard K Hite / Abstract: Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, ...Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, cell death, differentiation and fertilization. IPRs are jointly activated by inositol trisphosphate (IP) and their permeant ion, Ca. At high concentrations, however, Ca inhibits activity, ensuring precise spatiotemporal control over intracellular Ca. Despite extensive characterization of IPR, the mechanisms through which these molecules control channel gating have remained elusive. Here, we present structures of full-length human type 3 IPRs in ligand-bound and ligand-free states. Multiple IP-bound structures demonstrate that the large cytoplasmic domain provides a platform for propagation of long-range conformational changes to the ion-conduction gate. Structures in the presence of Ca reveal two Ca-binding sites that induce the disruption of numerous interactions between subunits, thereby inhibiting IPR. These structures thus provide a mechanistic basis for beginning to understand the regulation of IPR. | |||||||||
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_7980.map.gz | 193.1 MB | EMDB map data format | |
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Header (meta data) | emd-7980-v30.xml emd-7980.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_7980.png | 83.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7980 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7980 | HTTPS FTP |
-Related structure data
Related structure data | 7978C 7979C 7981C 7982C 7983C 7984C 7985C 7986C 7987C 7988C 7989C 7990C 7991C 7992C 7993C 7994C 7995C 7996C 6dqjC 6dqnC 6dqsC 6dqvC 6dqzC 6dr0C 6dr2C 6draC 6drcC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7980.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single subunit refinement of human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.088 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human type 3 inositol 1,4,5-trisphosphate receptor
Entire | Name: human type 3 inositol 1,4,5-trisphosphate receptor |
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Components |
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-Supramolecule #1: human type 3 inositol 1,4,5-trisphosphate receptor
Supramolecule | Name: human type 3 inositol 1,4,5-trisphosphate receptor / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK 293S GnTi / Recombinant plasmid: BacMam |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 Component:
Details: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA | ||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2 seconds prior to freezing. | ||||||||||||||||||
Details | ligand-free human type 3 inositol 1,4,5-trisphosphate receptor in detergent micelles |
-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: 0.0 mm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Specialist optics | Spherical aberration corrector: FEI Cs corrector / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1801 / Average exposure time: 8.0 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 211068 |
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CTF correction | Software - Name: CTFFIND |
Startup model | Type of model: OTHER / Details: CryoSPARC initial model |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: FREALIGN |
Final 3D classification | Number classes: 4 / Avg.num./class: 52767 / Software - Name: RELION |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: FREALIGN |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 81299 |
Details | Movie frames were aligned with MotionCor2 |