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- EMDB-7992: Cytoplasmic domain of low IP3 Ca2+ human type 3 1,4,5-inositol tr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7992 | |||||||||
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Title | Cytoplasmic domain of low IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor | |||||||||
![]() | Cytoplasmic domain of low IP3 Ca2 human type 3 1,4,5-inositol trisphosphate receptor | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Hite RK / Paknejad N | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 96.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7978C ![]() 7979C ![]() 7980C ![]() 7981C ![]() 7982C ![]() 7983C ![]() 7984C ![]() 7985C ![]() 7986C ![]() 7987C ![]() 7988C ![]() 7989C ![]() 7990C ![]() 7991C ![]() 7993C ![]() 7994C ![]() 7995C ![]() 7996C ![]() 6dqjC ![]() 6dqnC ![]() 6dqsC ![]() 6dqvC ![]() 6dqzC ![]() 6dr0C ![]() 6dr2C ![]() 6draC ![]() 6drcC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Cytoplasmic domain of low IP3 Ca2 human type 3 1,4,5-inositol trisphosphate receptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 2mM CaCl2 50 micromolar IP3 | |||||||||||||||||||||
Grid | Material: GOLD / 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 | human type 3 inositol 1,4,5-trisphosphate receptor in detergent micelles |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: 1409 / Average exposure time: 8.0 sec. / Average electron dose: 61.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |