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- EMDB-9246: Structure of full-length IP3R1 channel in Apo-state -

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Basic information

Entry
Database: EMDB / ID: EMD-9246
TitleStructure of full-length IP3R1 channel in Apo-state
Map datacryo-EM density map of IP3R1 in apo-state
Sample
  • Complex: Inositol 1,4,5-trisphosphate receptor
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsFan G / Baker MR / Wang Z / Seryshev AB / Ludtke SJ / Baker ML / Serysheva II
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM072804 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21AR063255 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS106968 United States
American Heart Association16GRNT2972000 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
National Science Foundation (NSF, United States)DBI-1356306 United States
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 /
Abstract: Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the ...Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the coupled interplay between binding of InsP and Ca that switches the ion conduction pathway between closed and open states to enable the passage of Ca through the channel. However, the molecular mechanism of how the receptor senses and decodes ligand-binding signals into gating motion remains unknown. Here, we present the electron cryo-microscopy structure of InsPR1 from rat cerebellum determined to 4.1 Å resolution in the presence of activating concentrations of Ca and adenophostin A (AdA), a structural mimetic of InsP and the most potent known agonist of the channel. Comparison with the 3.9 Å-resolution structure of InsPR1 in the Apo-state, also reported herein, reveals the binding arrangement of AdA in the tetrameric channel assembly and striking ligand-induced conformational rearrangements within cytoplasmic domains coupled to the dilation of a hydrophobic constriction at the gate. Together, our results provide critical insights into the mechanistic principles by which ligand-binding allosterically gates InsPR channel.
History
DepositionOct 22, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseDec 5, 2018-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9246.png

Downloads & links

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Map

FileDownload / File: emd_9246.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM density map of IP3R1 in apo-state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 200 pix.
= 252. Å		1.26 Å/pix.
x 200 pix.
= 252. Å		1.26 Å/pix.
x 200 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 LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-6.904124 - 10.5527115
Average (Standard dev.)0.056378666 (±0.36657882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

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/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-6.90410.5530.056

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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
Components
  • Complex: Inositol 1,4,5-trisphosphate receptor

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Supramolecule #1: Inositol 1,4,5-trisphosphate receptor

SupramoleculeName: Inositol 1,4,5-trisphosphate receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: tetrameric assembly
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Brain / Tissue: Cerebellum / Organelle: endoplasmic reticulum / Location in cell: membrane
Molecular weightTheoretical: 1.3 MDa

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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

BufferpH: 7.4
Details: 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
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unavailable
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Details0.1 mg/ml

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 93.0 K / Max: 93.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-17 / Number real images: 9823 / Average exposure time: 0.2 sec. / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 207914
CTF correctionSoftware - Name: EMAN2 (ver. 2.1)
Startup modelType of model: EMDB MAP
EMDB ID:

6369

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 100615
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2.1)
Final 3D classificationSoftware - Name: EMAN2 (ver. 2.1)

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