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- EMDB-9247: Structure of full-length IP3R1 channel in ligand-bound state -

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Basic information

Entry
Database: EMDB / ID: 9247
TitleStructure of full-length IP3R1 channel in ligand-bound state
Map dataCryo-EM densty map of IP3R1 in a ligand-bound state
SampleInositol 1,4,5-trisphosphate receptor:
inositol 1,4,5-trisphosphate receptor
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsFan G / Baker MR / Wang Z / Seryshev AB / Ludtke SJ / Baker ML / Serysheva II
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
DateDeposition: Oct 22, 2018 / Header (metadata) release: Nov 7, 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: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9247.png

Downloads & links

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Map

Fileemd_9247.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

Histogram

Histogram (log scale)
Contour Level:0.4 (by author), 0.4 (movie #1):
Minimum - Maximum-1.4814746 - 1.8334695
Average (Standard dev.)0.035191 (0.1394396)
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/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-1.4811.8330.035

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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

ProteinName: inositol 1,4,5-trisphosphate receptor / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer 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
pH: 7.4
Support filmunavailable
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
LensCs: 2 mm / Imaging 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: 14686

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 50903
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

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