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Basic information

Entry
Database: EMDB / ID: EMD-73210
TitleHuman type 2 IP3 receptor in the inactive-like state (IP3/ATP/Ca2+)
Map data
Sample
  • Complex: Inositol 1,4,5-trisphosphate receptor type 2
    • Protein or peptide: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
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: 3.42 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 3 receptor.
Authors: Liu C / Lan YJ / Kushner MG / Tang Q / Karakas E
History
DepositionOct 10, 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_73210.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.007682056 - 0.80788785
Average (Standard dev.)0.0050499844 (±0.010630273)
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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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: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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

MacromoleculeName: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 312.686125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTEKMSSFLY IGDIVSLYAE GSVNGFISTL GLVDDRCVVH PEAGDLANPP KKFRDCLFKV CPMNRYSAQK QYWKAKQAKQ GNHTEAALL KKLQHAAELE QKQNESENKK LLGEIVKYSN VIQLLHIKSN KYLTVNKRLP ALLEKNAMRV SLDAAGNEGS W FYIHPFWK ...String:
MTEKMSSFLY IGDIVSLYAE GSVNGFISTL GLVDDRCVVH PEAGDLANPP KKFRDCLFKV CPMNRYSAQK QYWKAKQAKQ GNHTEAALL KKLQHAAELE QKQNESENKK LLGEIVKYSN VIQLLHIKSN KYLTVNKRLP ALLEKNAMRV SLDAAGNEGS W FYIHPFWK LRSEGDNIVV GDKVVLMPVN AGQPLHASNI ELLDNPGCKE VNAVNCNTSW KITLFMKYSS YREDVLKGGD VV RLFHAEQ EKFLTCDEYE KKQHIFLRTT LRQSATSATS SKALWEIEVV HHDPCRGGAG QWNSLFRFKH LATGNYLAAE LNP DYRDAQ NEGKNVRDGV PPTSKKKRQA GEKIMYTLVS VPHGNDIASL FELDATTLQR ADCLVPRNSY VRLRHLCTNT WVTS TSIPI DTDEERPVML KIGTCQTKED KEAFAIVSVP LSEVRDLDFA NDANKVLATT VKKLENGTIT QNERRFVTKL LEDLI FFVA DVPNNGQEVL DVVITKPNRE RQKLMREQNI LAQVFGILKA PFKEKAGEGS MLRLEDLGDQ RYAPYKYMLR LCYRVL RHS QQDYRKNQEY IAKNFCVMQS QIGYDILAED TITALLHNNR KLLEKHITAK EIETFVSLLR RNREPRFLDY LSDLCVS NT TAIPVTQELI CKFMLSPGNA DILIQTKVVS MQADNPMESS ILSDDIDDEE VWLYWIDSNK EPHGKAIRHL AQEAKEGT K ADLEVLTYYR YQLNLFARMC LDRQYLAINQ ISTQLSVDLI LRCVSDESLP FDLRASFCRL MLHMHVDRDP QESVVPVRY ARLWTEIPTK ITIHEYDSIT DSSRNDMKRK FALTMEFVEE YLKEVVNQPF PFGDKEKNKL TFEVVHLARN LIYFGFYSFS ELLRLTRTL LAILDIVQAP MSSYFERLSK FQDGGNNVMR TIHGVGEMMT QMVLSRGSIF PMSVPDVPPS IHPSKQGSPT E HEDVTVMD TKLKIIEILQ FILSVRLDYR ISYMLSIYKK EFGEDNDNAE TSASGSPDTL LPSAIVPDID EIAAQAETMF AG RKEKNPV QLDDEGGRTF LRVLIHLIMH DYPPLLSGAL QLLFKHFSQR AEVLQAFKQV QLLVSNQDVD NYKQIKADLD QLR LTVEKS ELWVEKSSNY ENGEIGESQV KGGEEPIEES NILSPVQDGT KKPQIDSNKS NNYRIVKEIL IRLSKLCVQN KKCR NQHQR LLKNMGAHSV VLDLLQIPYE KNDEKMNEVM NLAHTFLQNF CRGNPQNQVL LHKHLNLFLT PGLLEAETMR HIFMN NYHL CNEISERVVQ HFVHCIETHG RHVEYLRFLQ TIVKADGKYV KKCQDMVMTE LINGGEDVLI FYNDRASFPI LLHMMC SER DRGDESGPLA YHITLVELLA ACTEGKNVYT EIKCNSLLPL DDIVRVVTHD DCIPEVKIAY VNFVNHCYVD TEVEMKE IY TSNHIWKLFE NFLVDMARVC NTTTDRKHAD IFLEKCVTES IMNIVSGFFN SPFSDNSTSL QTHQPVFIQL LQSAFRIY N CTWPNPAQKA SVESCIRTLA EVAKNRGIAI PVDLDSQVNT LFMKSHSNMV QRAAMGWRLS ARSGPRFKEA LGGPAWDYR NIIEKLQDVV ASLEHQFSPM MQAEFSVLVD VLYSPELLFP EGSDARIRCG AFMSKLINHT KKLMEKEEKL CIKILQTLRE MLEKKDSFV EEGNTLRKIL LNRYFKGDYS IGVNGHLSGA YSKTAQVGGS FSGQDSDKMG ISMSDIQCLL DKEGASELVI D VIVNTKND RIFSEGIFLG IALLEGGNTQ TQYSFYQQLH EQKKSEKFFK VLYDRMKAAQ KEIRSTVTVN TIDLGNKKRD DD NELMTSG PRMRVRDSTL HLKEGMKGQL TEASSATSKA YCVYRREMDP EIDIMCTGPE AGNTEEKSAE EVTMSPAIAI MQP ILRFLQ LLCENHNREL QNFLRNQNNK TNYNLVCETL QFLDCICGST TGGLGLLGLY INEKNVALVN QNLESLTEYC QGPC HENQT CIATHESNGI DIIIALILND INPLGKYRMD LVLQLKNNAS KLLLAIMESR HDSENAERIL FNMRPRELVD VMKNA YNQG LECDHGDDEG GDDGVSPKDV GHNIYILAHQ LARHNKLLQQ MLKPGSDPDE GDEALKYYAN HTAQIEIVRH DRTMEQ IVF PVPNICEYLT RESKCRVFNT TERDEQGSKV NDFFQQTEDL YNEMKWQKKI RNNPALFWFS RHISLWGSIS FNLAVFI NL AVALFYPFGD DGDEGTLSPL FSVLLWIAVA ICTSMLFFFS KPVGIRPFLV SIMLRSIYTI GLGPTLILLG AANLCNKI V FLVSFVGNRG TFTRGYRAVI LDMAFLYHVA YVLVCMLGLF VHEFFYSFLL FDLVYREETL LNVIKSVTRN GRSIILTAV LALILVYLFS IIGFLFLKDD FTMEVDRLKN RTPVTGSHQV PTMTLTTMME ACAKENCSPT IPASNTADEE YEDGIERTCD TLLMCIVTV LNQGLRNGGG VGDVLRRPSK DEPLFAARVV YDLLFYFIVI IIVLNLIFGV IIDTFADLRS EKQKKEEILK T TCFICGLE RDKFDNKTVS FEEHIKSEHN MWHYLYFIVL VKVKDPTEYT GPESYVAQMI VEKNLDWFPR MRAMSLVSNE GD SEQNEIR SLQEKLESTM SLVKQLSGQL AELKEQMTEQ RKNKQRLGFL GSNTPHVNHH MPPHASASNG LVPRGSAAAG WSH PQFEKG GGSGGGSGGS AWSHPQFEK

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

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Macromolecule #2: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

MacromoleculeName: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: I3P
Molecular weightTheoretical: 420.096 Da
Chemical component information

ChemComp-I3P:
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
4.0 mMCaCl2Calcium chloride

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, 1 mM ATP and 4 mM CaCl2
GridModel: Quantifoil R1.2/1.3 / 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: 11502 / 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 157230
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ynk:
Human type 2 IP3 receptor in the inactive-like state (IP3/ATP/Ca2+)

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