|Entry||Database: PDB / ID: 3jav|
|Title||Structure of full-length IP3R1 channel in the apo-state determined by single particle cryo-EM|
|Components||Inositol 1,4,5-trisphosphate receptor type 1|
|Keywords||TRANSPORT PROTEIN / inositol 1 / 4 / 5-trisphosphate receptor / calcium release channel / calcium signaling|
|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||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å|
|Authors||Fan, G. / Baker, M.L. / Wang, Z. / Baker, M.R. / Sinyagovskiy, P.A. / Chiu, W. / Ludtke, S.J. / Serysheva, I.I.|
|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||Molecule: |
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|PDBx/mmCIF format||3jav.cif.gz||1.1 MB||Display||PDBx/mmCIF format|
|PDB format||pdb3jav.ent.gz||596.6 KB||Display||PDB format|
|PDBx/mmJSON format||3jav.json.gz||Tree view||PDBx/mmJSON format|
|Summary document||3jav_validation.pdf.gz||800.5 KB||Display||wwPDB validaton report|
|Full document||3jav_full_validation.pdf.gz||1.1 MB||Display|
|Data in XML||3jav_validation.xml.gz||205.9 KB||Display|
|Data in CIF||3jav_validation.cif.gz||296.8 KB||Display|
-Related structure data
|Related structure data|
M: map data used to model this data
C: citing same article (ref.)
|Similar structure data|
|PDB pages||PDBj / wwPDB / NCBI|
|Related items in Molecule of the Month|
A: Inositol 1,4,5-trisphosphate receptor type 1
B: Inositol 1,4,5-trisphosphate receptor type 1
C: Inositol 1,4,5-trisphosphate receptor type 1
D: Inositol 1,4,5-trisphosphate receptor type 1
Mass: 313657.406 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P29994
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Inositol 1,4,5-trisphosphate receptor, type 1 / Type: COMPLEX / Details: homotetramer|
|Molecular weight||Value: 1.3 MDa / Experimental value: NO|
|Buffer solution||Name: 50 mM Tris-HCl, 0.4% CHAPS, 150 mM NaCl, 1 mM DTT, 1 mM EGTA, 1 mM EDTA|
Details: 50 mM Tris-HCl, 0.4% CHAPS, 150 mM NaCl, 1 mM DTT, 1 mM EGTA, 1 mM EDTA
|Specimen||Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: 400 mesh copper grids with thin carbon support|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 %|
Details: Blot once for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Method: blot once for 3 seconds
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Microscopy||Model: FEI POLARA 300 / Date: Jan 1, 2014|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 23000 X / Calibrated magnification: 30886 X / Nominal defocus max: 3500 nm / Nominal defocus min: 600 nm / Cs: 2 mm|
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
|Specimen holder||Specimen holder model: GATAN LIQUID NITROGEN / Temperature: 100 K / Temperature (max): 102 K / Temperature (min): 95 K|
|Image recording||Electron dose: 22 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)|
|EM imaging optics||Energyfilter name: FEI|
|Image scans||Num. digital images: 4160|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Relative weight: 1|
|CTF correction||Details: CTFFIND3|
|Symmetry||Point symmetry: C4 (4 fold cyclic)|
|3D reconstruction||Method: K-means clustering / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96106 / Nominal pixel size: 1.62 Å / Actual pixel size: 1.62 Å / Details: Applied symmetry: C4 / Symmetry type: POINT|
|Refinement step||Cycle: LAST|
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