|Entry||Database: PDB / ID: 7lhe|
|Title||Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state|
|Components||Inositol 1,4,5-trisphosphate receptor type 1|
|Keywords||MEMBRANE PROTEIN / Calcium channel / lipid nanodisc|
|Function / homology|
Function and homology information
Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 granule membrane / platelet dense tubular network / channel activator activity / 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 / 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 granule membrane / platelet dense tubular network / channel activator activity / ion channel regulator activity involved in G protein-coupled receptor signaling pathway / ligand-gated ion channel signaling pathway / negative regulation of calcium-mediated signaling / inositol phosphate-mediated signaling / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / calcineurin complex / 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 / transport vesicle membrane / nuclear inner membrane / calcium channel regulator activity / calcium-release channel activity / Ion homeostasis / dendrite development / 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 / positive regulation of insulin secretion / liver regeneration / post-embryonic development / sarcoplasmic reticulum / secretory granule membrane / synaptic membrane / positive regulation of neuron projection development / cellular response to cAMP / Schaffer collateral - CA1 synapse / calcium-mediated signaling / negative regulation of neuron death / presynapse / phospholipase C-activating G protein-coupled receptor signaling pathway / cell morphogenesis / cytoplasmic vesicle membrane / calcium ion transport / 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 / membrane raft / protein domain specific binding / intracellular membrane-bounded organelle / synapse / neuronal cell body / dendrite / protein-containing complex binding / nucleolus / calcium ion binding / endoplasmic reticulum membrane / 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
Chem-PLX / 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: 3.3 Å|
|Authors||Baker, M.R. / Fan, G. / Baker, M.L. / Serysheva, I.I.|
|Funding support|| United States, 7items |
|Citation||Journal: Commun Biol / Year: 2021|
Title: Cryo-EM structure of type 1 IPR channel in a lipid bilayer.
Authors: Mariah R Baker / Guizhen Fan / Alexander B Seryshev / Melina A Agosto / Matthew L Baker / Irina I Serysheva /
Abstract: Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved ...Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IPR1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IPR1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IPR1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating.
|Structure viewer||Molecule: |
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|PDBx/mmCIF format||7lhe.cif.gz||1.6 MB||Display||PDBx/mmCIF format|
|PDB format||pdb7lhe.ent.gz||1.3 MB||Display||PDB format|
|PDBx/mmJSON format||7lhe.json.gz||Tree view||PDBx/mmJSON format|
|Summary document||7lhe_validation.pdf.gz||1.8 MB||Display||wwPDB validaton report|
|Full document||7lhe_full_validation.pdf.gz||2 MB||Display|
|Data in XML||7lhe_validation.xml.gz||243 KB||Display|
|Data in CIF||7lhe_validation.cif.gz||359.3 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
D: Inositol 1,4,5-trisphosphate receptor type 1
C: Inositol 1,4,5-trisphosphate receptor type 1
B: Inositol 1,4,5-trisphosphate receptor type 1
Mass: 311848.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: cerebellum / References: UniProt: P29994
ChemComp-PLX / (
Mass: 767.132 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C42H89NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
|Has ligand of interest||Y|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex|
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
|Molecular weight||Value: 1.3 MDa / Experimental value: NO|
|Source (natural)||Organism: Rattus norvegicus (Norway rat) / Cellular location: membrane / Organ: cerebellum / Organelle: endoplasmic reticulum|
|Buffer solution||pH: 7.4|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid type: Quantifoil|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: TFS KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Calibrated magnification: 46943 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 0.2 sec. / Electron dose: 56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 22000|
|EM imaging optics||Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV|
|Image scans||Sampling size: 5 µm / Width: 3840 / Height: 3712 / Movie frames/image: 35 / Used frames/image: 2-35|
|Software||Name: PHENIX / Version: dev_svn: / Classification: refinement|
|CTF correction||Type: NONE|
|Symmetry||Point symmetry: C4 (4 fold cyclic)|
|3D reconstruction||Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 573723 / Symmetry type: POINT|
|Atomic model building||Protocol: FLEXIBLE FIT / Space: REAL|
|Atomic model building||PDB-ID: 6MU2|
|Refine LS restraints|
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