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- EMDB-7979: Cytoplasmic domain of human type 3 1,4,5-inositol trisphosphate r... -

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Basic information

Entry
Database: EMDB / ID: EMD-7979
TitleCytoplasmic domain of human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state
Map dataCytoplasmic domain focused refinement of human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state
Sample
  • Organelle or cellular component: human type 3 inositol 1,4,5-trisphosphate receptor
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 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-
UpdateDec 5, 2018-
Current statusDec 5, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0236
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0236
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7979.png

Downloads & links

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Map

FileDownload / File: emd_7979.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytoplasmic domain focused refinement of human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state
Voxel sizeX=Y=Z: 1.088 Å
Density
Contour LevelBy AUTHOR: 0.0236 / Movie #1: 0.0236
Minimum - Maximum-0.044043366 - 0.08833453
Average (Standard dev.)-0.00033636356 (±0.0019145029)
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/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0440.088-0.000

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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 chlorideSodium Chlorid
50.0 mMTrisTris(hydroxymethyl)aminomethane hydrochloride
2.0 mMDTT1,4-Dithiothreitol
0.06 percentDigitoninDigitonin
5.0 mMEGTAethylene glycol-bis(aminoethyl ether)-N,N,N',N'-tetraacetic acid

Details: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / 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.
Detailsligand-free human type 3 inositol 1,4,5-trisphosphate receptor in detergent micelles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.0 mm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsSpherical aberration corrector: FEI Cs corrector / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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 / Number real images: 1801 / Average exposure time: 8.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 211068
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER / Details: CryoSPARC initial model
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 52767 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 119904
DetailsMovie frames were aligned with MotionCor2

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