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- PDB-6mu2: Structure of full-length IP3R1 channel in the Apo-state -

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Basic information

Entry
Database: PDB / ID: 6mu2
TitleStructure of full-length IP3R1 channel in the Apo-state
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsMEMBRANE PROTEIN / inositol 1 / 4 / 5-trisphosphate receptor / calcium release channel / neuronal type 1
Function / homologyInositol 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 sourceRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSerysheva, I.I. / Fan, G. / Baker, M.R. / Wang, Z. / Seryshev, A. / Ludtke, S.J. / Baker, M.L.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Oct 22, 2018 / Release: Dec 5, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 5, 2018Structure modelrepositoryInitial release
1.1Dec 12, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)1,254,6304
Polyers1,254,6304
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Inositol 1,4,5-trisphosphate receptor type 1 / IP3 receptor isoform 1 / InsP3R1 / Type 1 inositol 1 / 4 / 5-trisphosphate receptor / Type 1 InsP3 receptor


Mass: 313657.406 Da / Num. of mol.: 4 / Source: (natural) Rattus norvegicus (Norway rat) / Organ: Brain / Tissue: cerebellum / References: UniProt: P29994

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Inositol 1,4,5-trisphosphate receptor / Type: COMPLEX / Details: tetrameric assembly / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 1.3 MDa / Experimental value: NO
Source (natural)Cellular location: membrane / Organ: Brain / Organelle: endoplasmic reticulum / Organism: Rattus norvegicus (Norway rat) / Tissue: Cerebellum
Buffer solutionDetails: 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
pH: 7.4
SpecimenConc.: 0.1 mg/ml / Details: Monodisperse sample / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Temperature (max): 93 kelvins / Temperature (min): 93 kelvins
Image recordingAverage 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 scansMovie frames/image: 30 / Used frames/image: 2-17

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4CTFFIND3CTF correction
7Cootmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIXmodel refinementReal Space Refine
14Pathwalkingmodel fitting
15Gorgonmodel fitting
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNumber of particles selected: 207914
SymmetryPoint symmetry: C4
3D reconstructionResolution: 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 buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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