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- PDB-9yli: IP3/ATP-bound human type 2 IP3 receptor in the preactivated state -

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Basic information

Entry
Database: PDB / ID: 9yli
TitleIP3/ATP-bound human type 2 IP3 receptor in the preactivated 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 / Ion homeostasis / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / FCERI mediated Ca+2 mobilization / phosphatidylinositol binding / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cellular response to cAMP / 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 / transmembrane transporter binding / response to hypoxia / 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
ADENOSINE-5'-TRIPHOSPHATE / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 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 3 receptor.
Authors: Liu, C. / Lan, Y.J. / Kushner, M.G. / Tang, Q. / Karakas, E.
History
DepositionOct 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)1,263,61516
Polymers1,259,6444
Non-polymers3,97112
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
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: 314911.062 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-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15O15P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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 supportGrid 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: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76484
Details: The Map is a composite map prepared using focused refinement maps.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 3.33 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00572376
ELECTRON MICROSCOPYf_angle_d0.4997836
ELECTRON MICROSCOPYf_dihedral_angle_d5.7959732
ELECTRON MICROSCOPYf_chiral_restr0.0411164
ELECTRON MICROSCOPYf_plane_restr0.00412408

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