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- EMDB-76250: Apo-IP3R2 Local Refinement of ARM1-HD Domains -

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Basic information

Entry
Database: EMDB / ID: EMD-76250
TitleApo-IP3R2 Local Refinement of ARM1-HD Domains
Map dataapo-IP3R2 local refinement of ARM1-HD domains
Sample
  • Organelle or cellular component: Inositol 1,4,5-trisphosphate receptor type 2
Keywordsion channel / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsSerysehva II / Baker MR / Fan G
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM153178 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153178-01S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM072804 United States
American Heart Association23CDA1048883 United States
Welch FoundationAU-2014-20220331 United States
Welch FoundationAU-2014-20250403 United States
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM insights into isoform-specific properties of the IP3R2 channel
Authors: Baker MR / Lin X / Fan G / Martinez-Chavez A / Wagner LE / Malik S / Allison T / Bell B / Seryshev AB / Cordero-Morales J / Baker ML / Yule DI / Serysheva II
History
DepositionMar 22, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76250.png

Downloads & links

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Map

FileDownload / File: emd_76250.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationapo-IP3R2 local refinement of ARM1-HD domains
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 440 pix.
= 475.2 Å		1.08 Å/pix.
x 440 pix.
= 475.2 Å		1.08 Å/pix.
x 440 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-6.6844716 - 10.04936
Average (Standard dev.)0.000331541 (±0.037578493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76250_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: apo-IP3R2 local refinement of ARM1-HD domains - half map A

Fileemd_76250_half_map_1.map
Annotationapo-IP3R2 local refinement of ARM1-HD domains - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: apo-IP3R2 local refinement of ARM1-HD domains - half map B

Fileemd_76250_half_map_2.map
Annotationapo-IP3R2 local refinement of ARM1-HD domains - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Inositol 1,4,5-trisphosphate receptor type 2

EntireName: Inositol 1,4,5-trisphosphate receptor type 2
Components
  • Organelle or cellular component: Inositol 1,4,5-trisphosphate receptor type 2

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Supramolecule #1: Inositol 1,4,5-trisphosphate receptor type 2

SupramoleculeName: Inositol 1,4,5-trisphosphate receptor type 2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.2 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

Concentration3 mg/mL
BufferpH: 7.4 / Details: 50mM Tris-HCl, 150 mM NaCl, 1mM DTT, 1mM EDTA
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailsimmuoaffinity purified, LMNG and lipid solubilized tetrameric ion channel protein

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-35 / Number grids imaged: 1 / Number real images: 8112 / Average electron dose: 1.43 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 46100 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 413650
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7)
Details: C4 particles symmetry expanded, mask subtraction, local refinement
Number images used: 294924
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 153.41 / Target criteria: fit to density

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