|Entry||Database: PDB / ID: 7t3q|
|Title||IP3 and ATP bound type 3 IP3 receptor in the pre-active B state|
|Components||Inositol 1,4,5-trisphosphate receptor type 3|
|Keywords||METAL TRANSPORT / IP3 receptor / calcium signaling|
|Function / homology|
Function and homology information
sensory perception of bitter taste / sensory perception of sweet taste / DAG and IP3 signaling / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / sensory perception of umami taste / platelet dense tubular network membrane / PLC beta mediated events / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis ...sensory perception of bitter taste / sensory perception of sweet taste / DAG and IP3 signaling / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / sensory perception of umami taste / platelet dense tubular network membrane / PLC beta mediated events / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / inositol hexakisphosphate binding / inositol 1,4,5 trisphosphate binding / nuclear outer membrane / CLEC7A (Dectin-1) induces NFAT activation / calcium-release channel activity / brush border / calcium ion homeostasis / Role of phospholipids in phagocytosis / Ion homeostasis / phosphatidylinositol binding / Sensory perception of sweet, bitter, and umami (glutamate) taste / Regulation of insulin secretion / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / long-term synaptic potentiation / VEGFR2 mediated cell proliferation / sarcoplasmic reticulum / secretory granule membrane / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / sensory perception of taste / response to calcium ion / memory / Ca2+ pathway / apical part of cell / myelin sheath / positive regulation of cytosolic calcium ion concentration / receptor complex / G protein-coupled receptor signaling pathway / neuronal cell body / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / nucleoplasm / membrane / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol 1,4,5-trisphosphate receptor type 3
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å|
|Authors||Schmitz, E.A. / Takahashi, H. / Karakas, E.|
|Funding support|| United States, 3items |
|Citation||Journal: Nat Commun / Year: 2022|
Title: Structural basis for activation and gating of IP receptors.
Authors: Emily A Schmitz / Hirohide Takahashi / Erkan Karakas /
Abstract: A pivotal component of the calcium (Ca) signaling toolbox in cells is the inositol 1,4,5-triphosphate (IP) receptor (IPR), which mediates Ca release from the endoplasmic reticulum (ER), controlling ...A pivotal component of the calcium (Ca) signaling toolbox in cells is the inositol 1,4,5-triphosphate (IP) receptor (IPR), which mediates Ca release from the endoplasmic reticulum (ER), controlling cytoplasmic and organellar Ca concentrations. IPRs are co-activated by IP and Ca, inhibited by Ca at high concentrations, and potentiated by ATP. However, the underlying molecular mechanisms are unclear. Here we report cryo-electron microscopy (cryo-EM) structures of human type-3 IPR obtained from a single dataset in multiple gating conformations: IP-ATP bound pre-active states with closed channels, IP-ATP-Ca bound active state with an open channel, and IP-ATP-Ca bound inactive state with a closed channel. The structures demonstrate how IP-induced conformational changes prime the receptor for activation by Ca, how Ca binding leads to channel opening, and how ATP modulates the activity, providing insights into the long-sought questions regarding the molecular mechanism underpinning receptor activation and gating.
|Structure viewer||Molecule: |
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|PDBx/mmCIF format||7t3q.cif.gz||1.4 MB||Display||PDBx/mmCIF format|
|PDB format||pdb7t3q.ent.gz||Display||PDB format|
|PDBx/mmJSON format||7t3q.json.gz||Tree view||PDBx/mmJSON format|
|Summary document||7t3q_validation.pdf.gz||1.7 MB||Display||wwPDB validaton report|
|Full document||7t3q_full_validation.pdf.gz||1.8 MB||Display|
|Data in XML||7t3q_validation.xml.gz||215.4 KB||Display|
|Data in CIF||7t3q_validation.cif.gz||328.4 KB||Display|
-Related structure data
|Related structure data|
M: map data used to model this data
C: citing same article (ref.)
|Similar structure data|
Similarity search - Function & homologyF&H Search
Similarity search - FunctionF&H Search
Similarity search - HomologyF&H Search
|PDB pages||PDBj / wwPDB / NCBI|
|Related items in Molecule of the Month|
A: Inositol 1,4,5-trisphosphate receptor type 3
B: Inositol 1,4,5-trisphosphate receptor type 3
C: Inositol 1,4,5-trisphosphate receptor type 3
D: Inositol 1,4,5-trisphosphate receptor type 3
Mass: 299325.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITPR3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14573
Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
|Has ligand of interest||N|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Inositol 1,4,5-trisphosphate receptor type 3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT|
|Molecular weight||Value: 1.2 MDa / Experimental value: NO|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Spodoptera frugiperda (fall armyworm)|
|Buffer solution||pH: 8 |
Details: IP3, ATP, and CaCl2 were added before cryo-grid preparation.
|Specimen||Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN 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: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm|
|Image recording||Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 42361|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 846122|
|Symmetry||Point symmetry: C4 (4 fold cyclic)|
|3D reconstruction||Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153765 / Num. of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Protocol: FLEXIBLE FIT / Space: REAL|
|Atomic model building||PDB-ID: 6UQK|
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