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- PDB-12ai: Structure of mammalian Type 2 Inositol 1,4,5-trisphosphate recept... -

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Basic information

Entry
Database: PDB / ID: 12ai
TitleStructure of mammalian Type 2 Inositol 1,4,5-trisphosphate receptor (IP3R2) in the presence of IP3/Ca2+/ATP
ComponentsInositol 1,4,5-trisphosphate-gated calcium channel ITPR2
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5-trisphosphate-gated calcium channel activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Ion homeostasis / inositol 1,4,5 trisphosphate binding / transport vesicle membrane / intracellularly gated calcium channel activity / cellular response to ethanol ...Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5-trisphosphate-gated calcium channel activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Ion homeostasis / inositol 1,4,5 trisphosphate binding / transport vesicle membrane / intracellularly gated calcium channel activity / cellular response to ethanol / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / phosphatidylinositol binding / cellular response to cAMP / secretory granule membrane / sarcoplasmic reticulum / calcium ion transport / scaffold protein binding / cell cortex / response to hypoxia / transmembrane transporter binding / signaling receptor complex / axon / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / plasma membrane / cytoplasm
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 / Chem-PLX / Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsSerysheva, I.I. / Baker, M.R. / Fan, G.
Funding support United States, 6items
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, M.R. / Lin, X. / Fan, G. / Martinez-Chavez, A. / Wagner, L.E. / Malik, S. / Allison, T. / Bell, B. / Seryshev, A.B. / Cordero-Morales, J. / Baker, M.L. / Yule, D.I. / Serysheva, I.I.
History
DepositionMar 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 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)1,238,61824
Polymers1,231,4194
Non-polymers7,20020
Water00
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

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Protein , 1 types, 4 molecules ABCD

#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 / 5- ...IP3 receptor isoform 2 / IP3R 2 / InsP3R2 / Inositol 1 / 4 / 5-trisphosphate receptor type 2 / 5-trisphosphate type V receptor / Type 2 inositol 1 / 5-trisphosphate receptor / Type 2 InsP3 receptor


Mass: 307854.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itpr2, Itpr5 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q9Z329

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Non-polymers , 5 types, 20 molecules

#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
#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-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
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H89NO8P / Comment: phospholipid*YM

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Details

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: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.2 MDa / Experimental value: YES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 GNTI- / Plasmid: BacMam
Buffer solutionpH: 7.4 / Details: 50mM Tris-HCl, 150 mM NaCl, 1mM DTT, 1mM EDTA
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: immuoaffinity purified, LMNG and lipid solubilized tetrameric ion channel protein
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K

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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: 130000 X / Calibrated magnification: 46100 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording

Imaging-ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 37329

IDAverage exposure time (sec.)Electron dose (e/Å2)Detector mode
181.43SUPER-RESOLUTION
271.66SUPER-RESOLUTION
381.43
Image scans
Movie frames/imageUsed frames/imageIDImage recording-IDEntry-ID
351-351112AI
301-302212AI
351-353312AI

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7particle selectionblob and template picker
2EPUimage acquisition
4cryoSPARC4.7CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARC4.7initial Euler assignment
11cryoSPARC4.7final Euler assignment
12cryoSPARC4.7classification
13cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6026377
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151391 / Symmetry type: POINT
Atomic model buildingB value: 135.9 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: fit to map
Atomic model buildingSource name: AlphaFold / Type: in silico model

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