[English] 日本語
Yorodumi
- PDB-9ynk: Human type 2 IP3 receptor in the inactive-like state (IP3/ATP/Ca2+) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ynk
TitleHuman type 2 IP3 receptor in the inactive-like state (IP3/ATP/Ca2+)
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: 3.42 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 10, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)1,253,57516
Polymers1,250,7454
Non-polymers2,83112
Water00
1


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

-
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: 312686.125 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.: 1 / 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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, 0.05 mM IP3, 1 mM ATP and 4 mM CaCl2
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
60.05 mMInositol 1,4,5-triphosphateIP31
71 mMAdenosine triphosphateATP1
84 mMCalcium chlorideCaCl21
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 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.

-
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: 11502

-
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: C1 (asymmetric)
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157230 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 3.42 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00338706
ELECTRON MICROSCOPYf_angle_d0.4352356
ELECTRON MICROSCOPYf_dihedral_angle_d5.4335318
ELECTRON MICROSCOPYf_chiral_restr0.0386049
ELECTRON MICROSCOPYf_plane_restr0.0036637

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more