|Entry||Database: EMDB / ID: EMD-6369|
|Title||Structure of full-length IP3R1 channel in the apo-state determined by single particle cryo-EM|
|Map data||Reconstruction of IP3R1/Calcium release channel from the rat cerebellum|
|Keywords||inositol 1 / 4 / 5-trisphosphate receptor / calcium release channel / single-particle cryo-EM / calcium signaling / 3D reconstruction|
|Function / homology|
Function and homology information
ion channel regulator activity involved in G protein-coupled receptor signaling pathway / Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / channel activator activity / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / platelet dense granule membrane ...ion channel regulator activity involved in G protein-coupled receptor signaling pathway / Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / channel activator activity / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / platelet dense granule membrane / negative regulation of calcium-mediated signaling / inositol phosphate-mediated signaling / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / calcineurin complex / epithelial fluid transport / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / regulation of postsynaptic cytosolic calcium ion concentration / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / endoplasmic reticulum calcium ion homeostasis / positive regulation of calcium ion transport / positive regulation of hepatocyte proliferation / nuclear inner membrane / transport vesicle membrane / calcium channel regulator activity / Ion homeostasis / calcium-release channel activity / dendrite development / ligand-gated ion channel signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / GABA-ergic synapse / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / release of sequestered calcium ion into cytosol / calcium channel inhibitor activity / phosphatidylinositol binding / liver regeneration / post-embryonic development / secretory granule membrane / sarcoplasmic reticulum / synaptic membrane / cellular response to cAMP / positive regulation of neuron projection development / Schaffer collateral - CA1 synapse / calcium-mediated signaling / negative regulation of neuron death / positive regulation of insulin secretion / cell morphogenesis / phospholipase C-activating G protein-coupled receptor signaling pathway / calcium ion transport / presynapse / nuclear envelope / cellular response to hypoxia / postsynapse / positive regulation of cytosolic calcium ion concentration / transmembrane transporter binding / protein phosphatase binding / response to hypoxia / postsynaptic density / positive regulation of apoptotic process / protein domain specific binding / membrane raft / intracellular membrane-bounded organelle / synapse / neuronal cell body / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif ...Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / Mir domain superfamily / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Ion transport domain / Ion transport protein / Armadillo-type fold
Similarity search - Domain/homology
Inositol 1,4,5-trisphosphate receptor type 1
Similarity search - Component
|Biological species||Rattus norvegicus (Norway rat)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.7 Å|
|Authors||Fan G / Baker ML / Wang Z / Baker MR / Sinyagovskiy PA / Chiu W / Ludtke SJ / Serysheva II|
|Citation||Journal: Nature / Year: 2015|
Title: Gating machinery of InsP3R channels revealed by electron cryomicroscopy.
Authors: Guizhen Fan / Matthew L Baker / Zhao Wang / Mariah R Baker / Pavel A Sinyagovskiy / Wah Chiu / Steven J Ludtke / Irina I Serysheva /
Abstract: Inositol-1,4,5-trisphosphate receptors (InsP3Rs) are ubiquitous ion channels responsible for cytosolic Ca(2+) signalling and essential for a broad array of cellular processes ranging from contraction ...Inositol-1,4,5-trisphosphate receptors (InsP3Rs) are ubiquitous ion channels responsible for cytosolic Ca(2+) signalling and essential for a broad array of cellular processes ranging from contraction to secretion, and from proliferation to cell death. Despite decades of research on InsP3Rs, a mechanistic understanding of their structure-function relationship is lacking. Here we present the first, to our knowledge, near-atomic (4.7 Å) resolution electron cryomicroscopy structure of the tetrameric mammalian type 1 InsP3R channel in its apo-state. At this resolution, we are able to trace unambiguously ∼85% of the protein backbone, allowing us to identify the structural elements involved in gating and modulation of this 1.3-megadalton channel. Although the central Ca(2+)-conduction pathway is similar to other ion channels, including the closely related ryanodine receptor, the cytosolic carboxy termini are uniquely arranged in a left-handed α-helical bundle, directly interacting with the amino-terminal domains of adjacent subunits. This configuration suggests a molecular mechanism for allosteric regulation of channel gating by intracellular signals.
|Structure viewer||EM map: |
-Downloads & links
|Map data||emd_6369.map.gz||23.1 MB||EMDB map data format|
|Header (meta data)||emd-6369-v30.xml|
|Summary document||emd_6369_validation.pdf.gz||310.4 KB||Display||EMDB validaton report|
|Full document||emd_6369_full_validation.pdf.gz||309.9 KB||Display|
|Data in XML||emd_6369_validation.xml.gz||6.3 KB||Display|
-Related structure data
|Related structure data|
M: atomic model generated by this map
C: citing same article (ref.)
|Similar structure data|
|EMDB pages||EMDB (EBI/PDBe) / EMDataResource|
|Related items in Molecule of the Month|
|File||Download / File: emd_6369.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Annotation||Reconstruction of IP3R1/Calcium release channel from the rat cerebellum|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.62 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire : Inositol 1,4,5-trisphosphate receptor, type 1
|Entire||Name: Inositol 1,4,5-trisphosphate receptor, type 1|
-Supramolecule #1000: Inositol 1,4,5-trisphosphate receptor, type 1
|Supramolecule||Name: Inositol 1,4,5-trisphosphate receptor, type 1 / type: sample / ID: 1000 |
Details: The sample was purified from rat cerebellum after solubilization with detergent; only freshly purified protein was used for cryo-EM visualization.
Oligomeric state: tetramer / Number unique components: 1
|Molecular weight||Theoretical: 1.3 MDa|
-Macromolecule #1: Inositol 1,4,5-trisphosphate receptor
|Macromolecule||Name: Inositol 1,4,5-trisphosphate receptor / type: protein_or_peptide / ID: 1 / Name.synonym: Calcium release channel / Details: detergent-solubilized protein / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No / Database: NCBI|
|Source (natural)||Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Tissue: cerebellum / Location in cell: endoplasmic reticulum membrane|
|Molecular weight||Experimental: 300 KDa / Theoretical: 330 KDa|
|Sequence||UniProtKB: Inositol 1,4,5-trisphosphate receptor type 1|
|Processing||single particle reconstruction|
|Buffer||pH: 7.4 |
Details: 50 mM Tris-HCl, pH 7.4, 0.4% CHAPS, 150 mM NaCl, 1 mM DTT, 1 mM EGTA, 1 mM EDTA
|Grid||Details: 400 mesh copper grids with thin carbon support|
|Vitrification||Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: blot once for 3 seconds|
|Microscope||FEI POLARA 300|
|Electron beam||Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||Calibrated magnification: 30886 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 23000|
|Specialist optics||Energy filter - Name: FEI|
|Sample stage||Specimen holder model: GATAN LIQUID NITROGEN|
|Temperature||Min: 95 K / Max: 102 K / Average: 100 K|
|Alignment procedure||Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.|
|Date||Jan 1, 2014|
|Image recording||Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 0.81 µm / Number real images: 4160 / Average electron dose: 22 e/Å2|
Details: Every image is the sum of 30 frames recorded with a direct electron detector.
Model: Tecnai Polara / Image courtesy: FEI Company
|CTF correction||Details: CTFFIND3|
|Final reconstruction||Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: OTHER / Software - Name: RELION_1.3, EMAN_2.1 / Details: The final map was generated from 96,106 particles. / Number images used: 96106|
|Details||Particle selection: EMAN2.1, CTF correction: CTFFIND3, initial model: EMAN2.1, refinement: RELION 1.3|
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