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- EMDB-76258: IP3R2 (+IP3/Ca2+/ATP) Local Refinement of ARM3-ILD-LNK domains -

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Basic information

Entry
Database: EMDB / ID: EMD-76258
TitleIP3R2 (+IP3/Ca2+/ATP) Local Refinement of ARM3-ILD-LNK domains
Map dataCIA-IP3R2 Local Refinement of ARM3-ILD-LNK 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: 3.34 Å
AuthorsSerysheva 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 IPR2 channel.
Authors: Mariah R Baker / Xiaoxuan Lin / Guizhen Fan / Ariel Martinez-Chavez / Larry E Wagner / Sundeep Malik / Tyler Allison / Briar Bell / Alexander B Seryshev / Julio Cordero-Morales / Matthew L ...Authors: Mariah R Baker / Xiaoxuan Lin / Guizhen Fan / Ariel Martinez-Chavez / Larry E Wagner / Sundeep Malik / Tyler Allison / Briar Bell / Alexander B Seryshev / Julio Cordero-Morales / Matthew L Baker / David I Yule / Irina I Serysheva /
Abstract: Calcium release through inositol 1,4,5-trisphosphate receptors (IPRs) is a fundamental signaling mechanism that regulates diverse cellular processes. Among the three mammalian IPR isoforms, IPR2 is ...Calcium release through inositol 1,4,5-trisphosphate receptors (IPRs) is a fundamental signaling mechanism that regulates diverse cellular processes. Among the three mammalian IPR isoforms, IPR2 is widely expressed, yet its structural basis for activation and regulation remains unclear. Here, we report cryo-EM structures of mammalian IPR2 in ligand-free (closed) and CaIP/ATP-bound (activated) states at 3.3 Å and 3.6 Å resolution, respectively. These structures define the architecture of IPR2 and reveal conformational transitions associated with channel activation. Although the IP-binding pocket is conserved, subtype-specific differences in IP affinity likely arise from conformational dynamics of the regulatory ARM2 domain. Comparative analyses of IPR isoforms identify subtype-specific allosteric networks and domain motions that underlie differential regulation. We further define the ATP-binding site and, through mutagenesis and electrophysiology, establish the structural basis for ATP modulation of channel activity. Together, these findings reveal mechanisms of IPR2 activation and subtype-specific regulation, providing a framework for understanding isoform-dependent Ca signaling.
History
DepositionMar 22, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76258.png

Downloads & links

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Map

FileDownload / File: emd_76258.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCIA-IP3R2 Local Refinement of ARM3-ILD-LNK domains
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-2.4308126 - 2.6471417
Average (Standard dev.)0.00013188536 (±0.007981697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76258_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: CIA-IP3R2 Local Refinement of ARM3-ILD-LNK domains - half map A

Fileemd_76258_half_map_1.map
AnnotationCIA-IP3R2 Local Refinement of ARM3-ILD-LNK domains - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CIA-IP3R2 Local Refinement of ARM3-ILD-LNK domains - half map B

Fileemd_76258_half_map_2.map
AnnotationCIA-IP3R2 Local Refinement of ARM3-ILD-LNK 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
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Digitization - Frames/image: 1-35 / #0 - Number grids imaged: 2 / #0 - Number real images: 37329 / #0 - Average exposure time: 8.0 sec. / #0 - Average electron dose: 1.43 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Digitization - Frames/image: 1-30 / #1 - Number grids imaged: 2 / #1 - Number real images: 37329 / #1 - Average exposure time: 7.0 sec. / #1 - Average electron dose: 1.66 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #2 - Digitization - Frames/image: 1-35 / #2 - Number grids imaged: 2 / #2 - Number real images: 37329 / #2 - Average exposure time: 8.0 sec. / #2 - 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

Image recording ID1
Particle selectionNumber selected: 6026377
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: 3.34 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: 605564
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: 135.9 / Target criteria: fit to map

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