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- EMDB-7995: Transmembrane domain of high IP3 Ca2+ human type 3 1,4,5-inositol... -

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Basic information

Entry
Database: EMDB / ID: EMD-7995
TitleTransmembrane domain of high IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor
Map dataTransmembrane domain of High IP3 Ca2 human type 3 1,4,5-inositol trisphosphate receptor
Sample
  • Organelle or cellular component: human type 3 inositol 1,4,5-trisphosphate receptor
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
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 /
Abstract: Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, ...Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, cell death, differentiation and fertilization. IPRs are jointly activated by inositol trisphosphate (IP) and their permeant ion, Ca. At high concentrations, however, Ca inhibits activity, ensuring precise spatiotemporal control over intracellular Ca. Despite extensive characterization of IPR, the mechanisms through which these molecules control channel gating have remained elusive. Here, we present structures of full-length human type 3 IPRs in ligand-bound and ligand-free states. Multiple IP-bound structures demonstrate that the large cytoplasmic domain provides a platform for propagation of long-range conformational changes to the ion-conduction gate. Structures in the presence of Ca reveal two Ca-binding sites that induce the disruption of numerous interactions between subunits, thereby inhibiting IPR. These structures thus provide a mechanistic basis for beginning to understand the regulation of IPR.
History
DepositionJun 11, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseAug 1, 2018-
UpdateNov 20, 2019-
Current statusNov 20, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7995.png

Downloads & links

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Map

FileDownload / File: emd_7995.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTransmembrane domain of High IP3 Ca2 human type 3 1,4,5-inositol trisphosphate receptor
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.083974354 - 0.15881811
Average (Standard dev.)0.00010431364 (±0.0023540414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.79202 Å
α=β=γ: 90.0 °

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/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0840.1590.000

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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
Components
  • Organelle or cellular component: human type 3 inositol 1,4,5-trisphosphate receptor

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Supramolecule #1: human type 3 inositol 1,4,5-trisphosphate receptor

SupramoleculeName: human type 3 inositol 1,4,5-trisphosphate receptor / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK 293S GnTi / Recombinant plasmid: BacMam

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
50.0 mMTrisTris(hydroxymethyl)aminomethane hydrochloride
2.0 mMDTT1,4-Dithiothreitol
0.06 percentDigitoninDigitonin
2.0 mMCaCl2Calcium Chloride
50.0 micromolarIP3inositol trisphosphate

Details: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 2mM CaCl2 50 micromolar IP3
GridMaterial: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2 seconds prior to freezing.
Detailshuman type 3 inositol 1,4,5-trisphosphate receptor in detergent micelles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 8.0 sec. / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMovie frames were aligned with MotionCor2
Particle selectionNumber selected: 170308
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER / Details: CryoSPARC initial model
Final reconstructionNumber classes used: 3 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 77871
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationNumber classes: 7 / Avg.num./class: 12380 / Software - Name: RELION

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