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- EMDB-9244: Structure of full-length IP3R1 channel in Apo-state (composite) -

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Basic information

Entry
Database: EMDB / ID: 9244
TitleStructure of full-length IP3R1 channel in Apo-state (composite)
Map datacryoEM structure of IP3R1 in an apo state
SampleInositol 1,4,5-trisphosphate receptor
  • Inositol 1,4,5-trisphosphate receptor 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
SourceRattus norvegicus (Norway rat) / Rat (rat)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSerysheva II / Fan G / Baker MR / Wang Z / Seryshev A / Ludtke SJ / Baker ML
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 ReportPDB-ID: 6mu2

SummaryFull reportAbout validation report
DateDeposition: Oct 22, 2018 / Header (metadata) release: Nov 14, 2018 / Map release: Dec 5, 2018 / Last update: Dec 12, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Map surface with fitted models
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9244.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.26 Å/pix.
= 252. Å
200 pix
1.26 Å/pix.
= 252. Å
200 pix
1.26 Å/pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-8.843095999999999 - 11.961499
Average (Standard dev.)0.0822998 (0.6726335)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 252.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-8.84311.9610.082

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Supplemental data

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Sample components

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Entire Inositol 1,4,5-trisphosphate receptor

EntireName: Inositol 1,4,5-trisphosphate receptor / Details: tetrameric assembly / Number of components: 2

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Component #1: protein, Inositol 1,4,5-trisphosphate receptor

ProteinName: Inositol 1,4,5-trisphosphate receptor / Details: tetrameric assemblyTetramer / Recombinant expression: No
MassTheoretical: 1.3 MDa
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #2: protein, Inositol 1,4,5-trisphosphate receptor type 1

ProteinName: Inositol 1,4,5-trisphosphate receptor type 1 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 313.657406 kDa
SourceSpecies: Rat (rat)
Source (natural)Organ or tissue: Brain

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 93.0 - 93.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 9823

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 65438
3D reconstructionSoftware: RELION / Resolution: 3.9 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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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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