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- PDB-6dqv: Class 2 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor -

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Basic information

Entry
Database: PDB / ID: 6dqv
TitleClass 2 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 / homologyRyanodine receptor-related / PLC beta mediated events / Inositol 1,4,5-trisphosphate/ryanodine receptor / RyR/IP3R Homology associated domain / Ion transport domain / RIH domain / Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / Mir domain superfamily / Ion transport protein ...Ryanodine receptor-related / PLC beta mediated events / Inositol 1,4,5-trisphosphate/ryanodine receptor / RyR/IP3R Homology associated domain / Ion transport domain / RIH domain / Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / Mir domain superfamily / Ion transport protein / RIH domain / MIR domain / RyR and IP3R Homology associated / MIR motif / MIR domain profile. / Inositol 1,4,5-trisphosphate/ryanodine receptor / Effects of PIP2 hydrolysis / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / CLEC7A (Dectin-1) induces NFAT activation / Ion homeostasis / VEGFR2 mediated cell proliferation / Regulation of insulin secretion / Ca2+ pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Role of phospholipids in phagocytosis / DAG and IP3 signaling / Elevation of cytosolic Ca2+ levels / sensory perception of sweet taste / sensory perception of bitter taste / platelet dense tubular network membrane / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / sensory perception of umami taste / calcium ion transport into cytosol / inositol hexakisphosphate binding / inositol 1,4,5 trisphosphate binding / nuclear outer membrane / calcium-release channel activity / regulation of cardiac conduction / brush border / phosphatidylinositol binding / long-term synaptic potentiation / regulation of insulin secretion / memory / response to calcium ion / protein heterooligomerization / positive regulation of cytosolic calcium ion concentration / receptor complex / apical part of cell / platelet activation / protein homooligomerization / myelin sheath / G-protein coupled receptor signaling pathway / neuronal cell body / endoplasmic reticulum membrane / nucleolus / calcium ion binding / endoplasmic reticulum / integral component of plasma membrane / membrane / nucleoplasm / plasma membrane / cytoplasm / Inositol 1,4,5-trisphosphate receptor type 3
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.82 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 11, 2018 / Release: Aug 1, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 1, 2018Structure modelrepositoryInitial release
1.1Aug 15, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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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
Polyers1,217,9554
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/peptide
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: (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 / Formula: Zn / Zinc
#3: Chemical
ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 4 / Formula: C6H15O15P3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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) / Plasmid: BacMam / Strain: HEK 293S GnTi
Buffer solutionDetails: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA 50 micromolar IP3
pH: 8
Buffer component
IDConc.NameFormulaBuffer ID
1150 mMSodium ChloridNaCl1
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
Details: ligand-free human type 3 inositol 1,4,5-trisphosphate receptor in detergent micelles
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins / Details: Blot for 2 seconds prior to freezing

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / 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) / Number of grids imaged: 1 / Number of real images: 4519
Image scansSampling size: 5 microns / Width: 7420 / Height: 7676 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameCategory
1RELIONparticle selection
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 selectionNumber of particles selected: 302966
SymmetryPoint symmetry: C4
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 40531 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 169 / Ref protocol: AB INITIO MODEL / Ref space: REAL / Target criteria: map-to-model FSC

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