|Entry||Database: PDB / ID: 6mu2|
|Title||Structure of full-length IP3R1 channel in the Apo-state|
|Components||Inositol 1,4,5-trisphosphate receptor type 1|
|Keywords||MEMBRANE PROTEIN / inositol 1 / 4 / 5-trisphosphate receptor / calcium release channel / neuronal type 1|
|Function / homology||Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RIH domain / Ion transport domain / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine receptor-related / Armadillo-type fold / MIR motif / Mir domain superfamily ...Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RIH domain / Ion transport domain / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine receptor-related / Armadillo-type fold / MIR motif / Mir domain superfamily / Ion transport protein / RIH domain / MIR domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / MIR domain profile. / smooth endoplasmic reticulum membrane / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / positive regulation of hepatocyte proliferation / inositol 1,4,5 trisphosphate binding / integral component of organelle membrane / positive regulation of calcium ion transport / calcium-release channel activity / synaptic membrane / integral component of endoplasmic reticulum membrane / GABA-ergic synapse / transport vesicle membrane / dendrite development / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / sarcoplasmic reticulum / presynapse / secretory granule membrane / positive regulation of neuron projection development / liver regeneration / cellular response to cAMP / negative regulation of neuron death / cytoplasmic vesicle membrane / postsynapse / nuclear envelope / cellular response to hypoxia / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / protein phosphatase binding / protein C-terminus binding / postsynaptic density / protein-containing complex binding / membrane raft / intracellular membrane-bounded organelle / positive regulation of apoptotic process / dendrite / endoplasmic reticulum membrane / neuronal cell body / calcium ion binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / plasma membrane / cytoplasm / Inositol 1,4,5-trisphosphate receptor type 1|
Function and homology information
|Specimen source||Rattus norvegicus (Norway rat)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution|
|Authors||Serysheva, I.I. / Fan, G. / Baker, M.R. / Wang, Z. / Seryshev, A. / Ludtke, S.J. / Baker, M.L.|
|Citation||Journal: Cell Res. / Year: 2018|
Title: Cryo-EM reveals ligand induced allostery underlying InsPR channel gating.
Authors: Guizhen Fan / Mariah R Baker / Zhao Wang / Alexander B Seryshev / Steven J Ludtke / Matthew L Baker / Irina I Serysheva
SummaryFull reportAbout validation report
|Date||Deposition: Oct 22, 2018 / Release: Dec 5, 2018|
|Structure viewer||Molecule: |
Downloads & links
B: Inositol 1,4,5-trisphosphate receptor type 1
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
Mass: 313657.406 Da / Num. of mol.: 4 / Source: (natural) Rattus norvegicus (Norway rat) / Organ: Brain / Tissue: cerebellum / References: UniProt: P29994
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: Inositol 1,4,5-trisphosphate receptor / Type: COMPLEX / Details: tetrameric assembly / Entity ID: 1 / Source: NATURAL|
|Molecular weight||Value: 1.3 MDa / Experimental value: NO|
|Source (natural)||Cellular location: membrane / Organ: Brain / Organelle: endoplasmic reticulum / Organism: Rattus norvegicus (Norway rat) / Tissue: Cerebellum|
|Buffer solution||Details: 50 mM Tris-HCl buffer (pH 7.4), 150 mM NaCl, 1 mM DTT, 0.4% CHAPS, 2 mM EGTA, 1 mM EDTA, protease inhibitors|
|Specimen||Conc.: 0.1 mg/ml / Details: Monodisperse sample / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/1|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TECNAI F30|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Specimen holder||Cryogen: NITROGEN|
Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Temperature (max): 93 kelvins / Temperature (min): 93 kelvins
|Image recording||Average exposure time: 0.2 sec. / Electron dose: 1.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 9823|
|Image scans||Movie frames/image: 30 / Used frames/image: 2-17|
|CTF correction||Type: PHASE FLIPPING ONLY|
|Particle selection||Number of particles selected: 207914|
|Symmetry||Point symmetry: C4|
|3D reconstruction||Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 65438|
Details: Image processing was performed independently using RELION and EMAN2 to near-atomic resolution in large regions of the structure. Local resolution assessment performed independently for each map revealed different domains were better resolved by each software package. To avoid human bias and extract the most information from each reconstruction the final map was a locally filtered average of the EMAN2 and RELION map. To combine the two maps, a local resolution filter, based on a windowed FSC local resolution assessment, was performed independently on the two maps. The two locally filtered maps were then averaged together. The local filtration determines the contribution of each map at each resolution in each region of the final composite map, permitting each map to dominate in regions where better self-consistency was obtained during refinement.
Symmetry type: POINT
|Atomic model building||Ref protocol: AB INITIO MODEL / Ref space: REAL|
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