|Entry||Database: EMDB / ID: 9243|
|Title||Structure of full-length IP3R1 channel bound with Adenophostin A (composite)|
|Map data||cryo-EM density map (composite) of IP3R1 in ligand-bound state|
|Sample||Inositol 1,4,5-trisphosphate receptor|
|Function / homology||MIR motif / RyR/IP3R Homology associated domain / MIR domain profile. / Inositol 1,4,5-trisphosphate/ryanodine receptor / RyR and IP3R Homology associated / MIR domain / RIH domain / Ion transport protein / Mir domain superfamily / Inositol 1,4,5-trisphosphate receptor ...MIR motif / RyR/IP3R Homology associated domain / MIR domain profile. / Inositol 1,4,5-trisphosphate/ryanodine receptor / RyR and IP3R Homology associated / MIR domain / RIH domain / Ion transport protein / Mir domain superfamily / Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RIH domain / Armadillo-type fold / Ryanodine receptor-related / Ion transport domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / calcium-release channel activity / synaptic membrane / transport vesicle membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / sarcoplasmic reticulum / secretory granule membrane / cellular response to cAMP / negative regulation of neuron death / nuclear envelope / cellular response to hypoxia / positive regulation of cytosolic calcium ion concentration / protein phosphatase binding / protein C-terminus binding / postsynaptic density / protein-containing complex binding / intracellular membrane-bounded organelle / membrane raft / dendrite / endoplasmic reticulum membrane / neuronal cell body / calcium ion binding / perinuclear region of cytoplasm / protein-containing complex / integral component of membrane / identical protein binding / plasma membrane / cytoplasm / Inositol 1,4,5-trisphosphate receptor type 1|
Function and homology information
|Source||Rattus norvegicus (Norway rat) / Rat (rat)|
|Method||single particle reconstruction / cryo EM / 4.1 Å resolution|
|Authors||Serysheva II / Fan G / Baker MR / Wang Z / Seryshev A / Ludtke SJ / Baker ML|
|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
|Validation Report||PDB-ID: 6mu1|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 22, 2018 / Header (metadata) release: Nov 14, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9243.map.gz (map file in CCP4 format, 32001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.26 Å|
CCP4 map header:
-Entire Inositol 1,4,5-trisphosphate receptor
|Entire||Name: Inositol 1,4,5-trisphosphate receptor / Details: tetrameric assembly / Number of components: 3|
-Component #1: protein, Inositol 1,4,5-trisphosphate receptor
|Protein||Name: Inositol 1,4,5-trisphosphate receptor / Details: tetrameric assemblyTetramer / Recombinant expression: No|
|Mass||Theoretical: 1.3 MDa|
|Source||Species: Rattus norvegicus (Norway rat)|
-Component #2: protein, Inositol 1,4,5-trisphosphate receptor type 1
|Protein||Name: Inositol 1,4,5-trisphosphate receptor type 1 / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 312.442 kDa|
|Source||Species: Rat (rat)|
-Component #3: ligand, Adenophostin A
|Ligand||Name: Adenophostin A / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 0.669322 kDa|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.1 mg/ml|
Buffer solution: 50 mM Tris-HCl buffer (pH 7.4), 150 mM NaCl, 1 mM DTT, 0.4% CHAPS,100 nM of AdA, 300 nM of Ca2+, protease inhibitors
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.3 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: GATAN LIQUID NITROGEN / Temperature: K ( 93.0 - 93.0 K)|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 14686|
|Processing||Method: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 179760|
|3D reconstruction||Software: RELION / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF|
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.
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