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- EMDB-73049: Human type 2 IP3 receptor apo state ligand binding domain (LBD) l... -

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Basic information

Entry
Database: EMDB / ID: EMD-73049
TitleHuman type 2 IP3 receptor apo state ligand binding domain (LBD) local refinement
Map dataSharpened map for LBD
Sample
  • Complex: Inositol 1,4,5-trisphosphate receptor type 2
KeywordsInositol 1 / 4 / 5-triphosphate / IP3 / receptor / calcium channel / type-2 / IP3R / IP3R-2 / ITPR2 / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsLiu C / Lan Y / Tang Q / Karakas E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141251 United States
CitationJournal: Nat Commun / Year: 2026
Title: Conformational landscape and ligand-dependent clustering of the human type 2 IP receptor.
Authors: Caifeng Liu / Yu-Jing Lan / Max G Kushner / Qingyu Tang / Erkan Karakas /
Abstract: Inositol 1,4,5-trisphosphate (IP) receptors (IPRs) are tetrameric ER Ca channels that shape intracellular Ca signaling in response to IP, regulating diverse physiological processes. The structural ...Inositol 1,4,5-trisphosphate (IP) receptors (IPRs) are tetrameric ER Ca channels that shape intracellular Ca signaling in response to IP, regulating diverse physiological processes. The structural basis for subtype-specific regulation among the three subtypes (IPR-1-3) remains incompletely understood due to the lack of IPR-2 structures. Here, we report cryo-electron microscopy (cryo-EM) structures of human IPR-2 in distinct conformations in the presence and absence of IP, Ca, and ATP. These structures define the conformational landscape of IPR-2, delineate ligand-binding interactions, and reveal shared architectural features alongside isoform-specific differences. We also resolve ligand-dependent IPR-2 assemblies, identifying a conformation-dependent inter-channel interface. Live-cell imaging demonstrates that IPR-2 undergoes clustering following ligand-induced Ca release, and disruption of this interface selectively abolishes clustering without impairing channel activity. Together, these findings provide a structural framework for human IPR-2 and establish a mechanism linking ligand-dependent conformational changes to inter-channel interactions and post-activation cellular clustering.
History
DepositionOct 7, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73049.png

Downloads & links

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Map

FileDownload / File: emd_73049.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map for LBD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 420.864 Å		0.82 Å/pix.
x 512 pix.
= 420.864 Å		0.82 Å/pix.
x 512 pix.
= 420.864 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.64405626 - 0.78588736
Average (Standard dev.)0.0003276487 (±0.009968906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 420.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73049_msk_1.map
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Additional map: Unsharpened Map

Fileemd_73049_additional_1.map
AnnotationUnsharpened Map
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Half map: #1

Fileemd_73049_half_map_1.map
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Half map: #2

Fileemd_73049_half_map_2.map
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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
  • Complex: 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: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Protein was reconstituted in MSP1E3D1/DOPC nanodiscs
Source (natural)Organism: Homo sapiens (human)
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

Concentration2.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.2 MNaClSodium Chloride
0.02 MTris-HClTris-HCl buffer
0.005 MEDTAEDTA
0.002 MDTTDTT
0.025 %FC-8fluorinated Fos-Choline-8

Details: 200 mM NaCl, 20 mM Tris-HCl pH 8.0, 5 mM EDTA pH 8.0, 2 mM DTT, 0.025% fluorinated Fos-Choline-8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: PELCO 595 filter paper (Ted Pella, prod. no. 47000-100) was used for vitrification..
DetailsThe sample was reconstituted in MSP1E3D1/DOPC nanodiscs

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11634 / Average electron dose: 54.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Particles were symmetry expanded prior to local refinement.
Number images used: 524012
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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