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- EMDB-73223: Human type 2 IP3 receptor in the intermediate state 3 (IP3/ATP) -

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Basic information

Entry
Database: EMDB / ID: EMD-73223
TitleHuman type 2 IP3 receptor in the intermediate state 3 (IP3/ATP)
Map dataUnsharpened Map
Sample
  • Complex: Inositol 1,4,5-trisphosphate receptor type 2
    • Protein or peptide: Human type 2 IP3 receptor
KeywordsInositol 1 / 4 / 5-triphosphate / IP3 / receptor / calcium channel / type-2 / IP3R / IP3R-2 / ITPR2 / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.47 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 11, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73223.png

Downloads & links

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Map

FileDownload / File: emd_73223.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened Map
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.033307515 - 0.078769624
Average (Standard dev.)0.0004310207 (±0.0044449004)
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_73223_msk_1.map
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Additional map: Sharpened Map

Fileemd_73223_additional_1.map
AnnotationSharpened Map
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Half map: #1

Fileemd_73223_half_map_1.map
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Half map: #2

Fileemd_73223_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
    • Protein or peptide: Human type 2 IP3 receptor

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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: all
Details: Protein was reconstituted in MSP1E3D1/DOPC nanodiscs
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: Human type 2 IP3 receptor

MacromoleculeName: Human type 2 IP3 receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTEKMSSFLY IGDIVSLYAE GSVNGFISTL GLVDDRCVVH PEAGDLANPP KKFRDCLFKV CPMNRYSAQK QYWKAKQAKQ GNHTEAALLK KLQHAAELEQ KQNESENKKL LGEIVKYSNV IQLLHIKSNK YLTVNKRLPA LLEKNAMRVS LDAAGNEGSW FYIHPFWKLR ...String:
MTEKMSSFLY IGDIVSLYAE GSVNGFISTL GLVDDRCVVH PEAGDLANPP KKFRDCLFKV CPMNRYSAQK QYWKAKQAKQ GNHTEAALLK KLQHAAELEQ KQNESENKKL LGEIVKYSNV IQLLHIKSNK YLTVNKRLPA LLEKNAMRVS LDAAGNEGSW FYIHPFWKLR SEGDNIVVGD KVVLMPVNAG QPLHASNIEL LDNPGCKEVN AVNCNTSWKI TLFMKYSSYR EDVLKGGDVV RLFHAEQEKF LTCDEYEKKQ HIFLRTTLRQ SATSATSSKA LWEIEVVHHD PCRGGAGQWN SLFRFKHLAT GNYLAAELNP DYRDAQNEGK NVRDGVPPTS KKKRQAGEKI MYTLVSVPHG NDIASLFELD ATTLQRADCL VPRNSYVRLR HLCTNTWVTS TSIPIDTDEE RPVMLKIGTC QTKEDKEAFA IVSVPLSEVR DLDFANDANK VLATTVKKLE NGTITQNERR FVTKLLEDLI FFVADVPNNG QEVLDVVITK PNRERQKLMR EQNILAQVFG ILKAPFKEKA GEGSMLRLED LGDQRYAPYK YMLRLCYRVL RHSQQDYRKN QEYIAKNFCV MQSQIGYDIL AEDTITALLH NNRKLLEKHI TAKEIETFVS LLRRNREPRF LDYLSDLCVS NTTAIPVTQE LICKFMLSPG NADILIQTKV VSMQADNPME SSILSDDIDD EEVWLYWIDS NKEPHGKAIR HLAQEAKEGT KADLEVLTYY RYQLNLFARM CLDRQYLAIN QISTQLSVDL ILRCVSDESL PFDLRASFCR LMLHMHVDRD PQESVVPVRY ARLWTEIPTK ITIHEYDSIT DSSRNDMKRK FALTMEFVEE YLKEVVNQPF PFGDKEKNKL TFEVVHLARN LIYFGFYSFS ELLRLTRTLL AILDIVQAPM SSYFERLSKF QDGGNNVMRT IHGVGEMMTQ MVLSRGSIFP MSVPDVPPSI HPSKQGSPTE HEDVTVMDTK LKIIEILQFI LSVRLDYRIS YMLSIYKKEF GEDNDNAETS ASGSPDTLLP SAIVPDIDEI AAQAETMFAG RKEKNPVQLD DEGGRTFLRV LIHLIMHDYP PLLSGALQLL FKHFSQRAEV LQAFKQVQLL VSNQDVDNYK QIKADLDQLR LTVEKSELWV EKSSNYENGE IGESQVKGGE EPIEESNILS PVQDGTKKPQ IDSNKSNNYR IVKEILIRLS KLCVQNKKCR NQHQRLLKNM GAHSVVLDLL QIPYEKNDEK MNEVMNLAHT FLQNFCRGNP QNQVLLHKHL NLFLTPGLLE AETMRHIFMN NYHLCNEISE RVVQHFVHCI ETHGRHVEYL RFLQTIVKAD GKYVKKCQDM VMTELINGGE DVLIFYNDRA SFPILLHMMC SERDRGDESG PLAYHITLVE LLAACTEGKN VYTEIKCNSL LPLDDIVRVV THDDCIPEVK IAYVNFVNHC YVDTEVEMKE IYTSNHIWKL FENFLVDMAR VCNTTTDRKH ADIFLEKCVT ESIMNIVSGF FNSPFSDNST SLQTHQPVFI QLLQSAFRIY NCTWPNPAQK ASVESCIRTL AEVAKNRGIA IPVDLDSQVN TLFMKSHSNM VQRAAMGWRL SARSGPRFKE ALGGPAWDYR NIIEKLQDVV ASLEHQFSPM MQAEFSVLVD VLYSPELLFP EGSDARIRCG AFMSKLINHT KKLMEKEEKL CIKILQTLRE MLEKKDSFVE EGNTLRKILL NRYFKGDYSI GVNGHLSGAY SKTAQVGGSF SGQDSDKMGI SMSDIQCLLD KEGASELVID VIVNTKNDRI FSEGIFLGIA LLEGGNTQTQ YSFYQQLHEQ KKSEKFFKVL YDRMKAAQKE IRSTVTVNTI DLGNKKRDDD NELMTSGPRM RVRDSTLHLK EGMKGQLTEA SSATSKAYCV YRREMDPEID IMCTGPEAGN TEEKSAEEVT MSPAIAIMQP ILRFLQLLCE NHNRELQNFL RNQNNKTNYN LVCETLQFLD CICGSTTGGL GLLGLYINEK NVALVNQNLE SLTEYCQGPC HENQTCIATH ESNGIDIIIA LILNDINPLG KYRMDLVLQL KNNASKLLLA IMESRHDSEN AERILFNMRP RELVDVMKNA YNQGLECDHG DDEGGDDGVS PKDVGHNIYI LAHQLARHNK LLQQMLKPGS DPDEGDEALK YYANHTAQIE IVRHDRTMEQ IVFPVPNICE YLTRESKCRV FNTTERDEQG SKVNDFFQQT EDLYNEMKWQ KKIRNNPALF WFSRHISLWG SISFNLAVFI NLAVALFYPF GDDGDEGTLS PLFSVLLWIA VAICTSMLFF FSKPVGIRPF LVSIMLRSIY TIGLGPTLIL LGAANLCNKI VFLVSFVGNR GTFTRGYRAV ILDMAFLYHV AYVLVCMLGL FVHEFFYSFL LFDLVYREET LLNVIKSVTR NGRSIILTAV LALILVYLFS IIGFLFLKDD FTMEVDRLKN RTPVTGSHQV PTMTLTTMME ACAKENCSPT IPASNTADEE YEDGIERTCD TLLMCIVTVL NQGLRNGGGV GDVLRRPSKD EPLFAARVVY DLLFYFIVII IVLNLIFGVI IDTFADLRSE KQKKEEILKT TCFICGLERD KFDNKTVSFE EHIKSEHNMW HYLYFIVLVK VKDPTEYTGP ESYVAQMIVE KNLDWFPRMR AMSLVSNEGD SEQNEIRSLQ EKLESTMSLV KQLSGQLAEL KEQMTEQRKN KQRLGFLGSN TPHVNHHMPP HASASNGLVP RGSAAAGWSH PQFEKGGGSG GGSGGSAWSH PQFEK

UniProtKB: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2

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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
0.05 mMIP3inositol 1,4,5-triphosphate
1.0 mMATPAdenosine triphosphate

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, 0.05 mM IP3, and 1 mM ATP
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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34143
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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