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- PDB-6dqn: Class 1 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor -

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Basic information

Entry
Database: PDB / ID: 6dqn
TitleClass 1 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
ComponentsInositol 1,4,5-trisphosphate receptor type 3
KeywordsMETAL TRANSPORT / Ion channel / Calcium channel
Function / homology
Function and homology information


sensory perception of bitter taste / sensory perception of sweet taste / DAG and IP3 signaling / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / sensory perception of umami taste / platelet dense tubular network membrane / PLC beta mediated events / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis ...sensory perception of bitter taste / sensory perception of sweet taste / DAG and IP3 signaling / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / sensory perception of umami taste / platelet dense tubular network membrane / PLC beta mediated events / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / inositol hexakisphosphate binding / inositol 1,4,5 trisphosphate binding / nuclear outer membrane / CLEC7A (Dectin-1) induces NFAT activation / calcium-release channel activity / brush border / calcium ion homeostasis / Role of phospholipids in phagocytosis / Ion homeostasis / phosphatidylinositol binding / Sensory perception of sweet, bitter, and umami (glutamate) taste / Regulation of insulin secretion / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / long-term synaptic potentiation / VEGFR2 mediated cell proliferation / sarcoplasmic reticulum / secretory granule membrane / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / sensory perception of taste / response to calcium ion / memory / Ca2+ pathway / apical part of cell / myelin sheath / positive regulation of cytosolic calcium ion concentration / receptor complex / G protein-coupled receptor signaling pathway / neuronal cell body / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / nucleoplasm / membrane / 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 superfamily / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol 1,4,5-trisphosphate receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsHite, R.K. / Paknejad, N.
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structural basis for the regulation of inositol trisphosphate receptors by Ca and IP.
Authors: Navid Paknejad / Richard K Hite /
Abstract: Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, ...Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, cell death, differentiation and fertilization. IPRs are jointly activated by inositol trisphosphate (IP) and their permeant ion, Ca. At high concentrations, however, Ca inhibits activity, ensuring precise spatiotemporal control over intracellular Ca. Despite extensive characterization of IPR, the mechanisms through which these molecules control channel gating have remained elusive. Here, we present structures of full-length human type 3 IPRs in ligand-bound and ligand-free states. Multiple IP-bound structures demonstrate that the large cytoplasmic domain provides a platform for propagation of long-range conformational changes to the ion-conduction gate. Structures in the presence of Ca reveal two Ca-binding sites that induce the disruption of numerous interactions between subunits, thereby inhibiting IPR. These structures thus provide a mechanistic basis for beginning to understand the regulation of IPR.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type

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Structure visualization

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Assembly

Deposited unit
A: Inositol 1,4,5-trisphosphate receptor type 3
B: Inositol 1,4,5-trisphosphate receptor type 3
C: Inositol 1,4,5-trisphosphate receptor type 3
D: Inositol 1,4,5-trisphosphate receptor type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,219,89712
Polymers1,217,9554
Non-polymers1,9428
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Inositol 1,4,5-trisphosphate receptor type 3 / IP3 receptor isoform 3 / InsP3R3 / Type 3 inositol 1 / 4 / 5-trisphosphate receptor / Type 3 InsP3 receptor


Mass: 304488.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITPR3 / Production host: Homo sapiens (human) / References: UniProt: Q14573
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15O15P3

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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: human type 3 inositol 1,4,5-trisphosphate receptor / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK 293S GnTi / Plasmid: BacMam
Buffer solutionpH: 8
Details: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA 50 micromolar IP3
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChloridNaClSodium chloride1
250 mMTris(hydroxymethyl)aminomethane hydrochlorideTris1
32 mM1,4-DithiothreitolDTT1
40.06 percentDigitoninDigitonin1
55 mMethylene glycol-bis(aminoethyl ether)-N,N,N',N'-tetraacetic acidEGTA1
650 micromolarinositol triphosphateIP31
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: ligand-free human type 3 inositol 1,4,5-trisphosphate receptor in detergent micelles
Specimen supportGrid material: GOLD
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Blot for 2 seconds prior to freezing

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 61 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1801
Image scansSampling size: 5 µm / Width: 7420 / Height: 7676 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9FREALIGNinitial Euler assignment
10FREALIGNfinal Euler assignment
11RELIONclassification
12FREALIGN3D reconstruction
13PHENIXmodel refinement
Image processingDetails: Movie frames were aligned with MotionCor2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 302966
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38777 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 116.1 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: map-to-model FSC

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