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- PDB-9ykk: Human type 2 IP3 receptor in apo state -

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Basic information

Entry
Database: PDB / ID: 9ykk
TitleHuman type 2 IP3 receptor in apo state
ComponentsInositol 1,4,5-trisphosphate-gated calcium channel ITPR2
KeywordsTRANSPORT PROTEIN / Inositol 1 / 4 / 5-triphosphate / IP3 / receptor / calcium channel / type-2 / IP3R / IP3R-2 / ITPR2
Function / homology
Function and homology information


calcium ion transmembrane transporter activity / DAG and IP3 signaling / inositol 1,4,5-trisphosphate-gated calcium channel activity / platelet dense tubular network membrane / Effects of PIP2 hydrolysis / PLC beta mediated events / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / transport vesicle membrane / CLEC7A (Dectin-1) induces NFAT activation ...calcium ion transmembrane transporter activity / DAG and IP3 signaling / inositol 1,4,5-trisphosphate-gated calcium channel activity / platelet dense tubular network membrane / Effects of PIP2 hydrolysis / PLC beta mediated events / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / transport vesicle membrane / CLEC7A (Dectin-1) induces NFAT activation / Role of phospholipids in phagocytosis / release of sequestered calcium ion into cytosol / Ion homeostasis / FCERI mediated Ca+2 mobilization / cellular response to cAMP / sarcoplasmic reticulum membrane / phosphatidylinositol binding / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / secretory granule membrane / VEGFR2 mediated cell proliferation / sarcoplasmic reticulum / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / scaffold protein binding / Ca2+ pathway / cell cortex / response to hypoxia / transmembrane transporter binding / signaling receptor complex / calcium ion binding / endoplasmic reticulum membrane / signal transduction / ATP binding / membrane / plasma membrane
Similarity search - Function
Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif ...Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / Ion transport domain / Ion transport protein / Armadillo-type fold
Similarity search - Domain/homology
Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsLiu, C. / Lan, Y. / Tang, Q. / Karakas, E.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
B: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
C: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
D: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,259,2258
Polymers1,258,9634
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2 / IP3 receptor isoform 2 / IP3R 2 / InsP3R2 / Inositol 1 / 4 / 5-trisphosphate receptor type 2 / Type ...IP3 receptor isoform 2 / IP3R 2 / InsP3R2 / Inositol 1 / 4 / 5-trisphosphate receptor type 2 / Type 2 inositol 1 / 5-trisphosphate receptor / Type 2 InsP3 receptor


Mass: 314740.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITPR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14571
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY
Sequence detailsA stretch of UNK residues is present in the model due to insufficient density to assign the ...A stretch of UNK residues is present in the model due to insufficient density to assign the sequence unambiguously.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Inositol 1,4,5-trisphosphate receptor type 2 / Type: COMPLEX
Details: Protein was reconstituted in MSP1E3D1/DOPC nanodiscs
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.2 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 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
Buffer component
IDConc.NameFormulaBuffer-ID
10.2 MSodium ChlorideNaCl1
20.02 MTris-HCl bufferTris-HCl1
30.005 MEDTAEDTA1
40.002 MDTTDTT1
50.025 %fluorinated Fos-Choline-8FC-81
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was reconstituted in MSP1E3D1/DOPC nanodiscs
Specimen supportDetails: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: PELCO 595 filter paper (Ted Pella, prod. no. 47000-100) was used for vitrification.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11634

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131003 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00372300
ELECTRON MICROSCOPYf_angle_d0.42197680
ELECTRON MICROSCOPYf_dihedral_angle_d4.0329488
ELECTRON MICROSCOPYf_chiral_restr0.03811148
ELECTRON MICROSCOPYf_plane_restr0.00312432

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