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- EMDB-7982: Cytoplasmic domain of class 1 IP3-bound human type 3 1,4,5-inosit... -

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Basic information

Entry
Database: EMDB / ID: 7982
TitleCytoplasmic domain of class 1 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Map dataCytoplasmic domain of class 1 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Samplehuman type 3 inositol 1,4,5-trisphosphate receptor:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.26 Å resolution
AuthorsHite RK / Paknejad N
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis for the regulation of inositol trisphosphate receptors by Ca and IP.
Authors: Navid Paknejad / Richard K Hite
DateDeposition: Jun 11, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: Aug 1, 2018 / Last update: Aug 15, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0338
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0338
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7982.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.09 Å/pix.
= 417.792 Å
384 pix
1.09 Å/pix.
= 417.792 Å
384 pix
1.09 Å/pix.
= 417.792 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density
Contour Level:0.0338 (by author), 0.0338 (movie #1):
Minimum - Maximum-0.15532099 - 0.25137174
Average (Standard dev.)0.00006459509 (0.002487358)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.0.0.
Limit383.383.383.
Spacing384384384
CellA=B=C: 417.79202 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z417.792417.792417.792
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1550.2510.000

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Supplemental data

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Sample components

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Entire human type 3 inositol 1,4,5-trisphosphate receptor

EntireName: human type 3 inositol 1,4,5-trisphosphate receptor / Number of components: 1

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Component #1: cellular-component, human type 3 inositol 1,4,5-trisphosphate receptor

Cellular-componentName: human type 3 inositol 1,4,5-trisphosphate receptor / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: BacMam / Strain: HEK 293S GnTi

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 8 mg/ml
Buffer solution: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA 50 micromolar IP3
pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % / Details: Blot for 2 seconds prior to freezing.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 61 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1801 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 428144 / Details: Movie frames were aligned with MotionCor2
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF

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