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- PDB-5x9z: Crystal structure of inositol 1,4,5-trisphosphate receptor large ... -

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Basic information

Entry
Database: PDB / ID: 5x9z
TitleCrystal structure of inositol 1,4,5-trisphosphate receptor large cytosolic domain
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsMETAL TRANSPORT / receptor channel calcium
Function / homology
Function and homology information


cGMP effects / Effects of PIP2 hydrolysis / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / platelet dense tubular network / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / inositol 1,4,5-trisphosphate-gated calcium channel activity ...cGMP effects / Effects of PIP2 hydrolysis / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / platelet dense tubular network / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / inositol 1,4,5-trisphosphate-gated calcium channel activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / calcium import into the mitochondrion / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / negative regulation of calcium-mediated signaling / Ion homeostasis / endoplasmic reticulum calcium ion homeostasis / nuclear inner membrane / transport vesicle membrane / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / regulation of cytosolic calcium ion concentration / single fertilization / calcium channel inhibitor activity / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / sarcoplasmic reticulum / post-embryonic development / positive regulation of insulin secretion / Schaffer collateral - CA1 synapse / cell morphogenesis / calcium ion transport / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / protein homotetramerization / response to hypoxia / postsynaptic density / positive regulation of apoptotic process / protein domain specific binding / synapse / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / ATP binding / metal ion binding / 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 / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Inositol 1,4,5-trisphosphate-gated calcium channel ITPR1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.311 Å
AuthorsHamada, K. / Miyatake, H. / Terauchi, A. / Mikoshiba, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS15K06791 Japan
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography
Authors: Hamada, K. / Miyatake, H. / Terauchi, A. / Mikoshiba, K.
History
DepositionMar 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol 1,4,5-trisphosphate receptor type 1
B: Inositol 1,4,5-trisphosphate receptor type 1


Theoretical massNumber of molelcules
Total (without water)504,7552
Polymers504,7552
Non-polymers00
Water00
1
A: Inositol 1,4,5-trisphosphate receptor type 1


Theoretical massNumber of molelcules
Total (without water)252,3771
Polymers252,3771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol 1,4,5-trisphosphate receptor type 1


Theoretical massNumber of molelcules
Total (without water)252,3771
Polymers252,3771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.503, 221.726, 318.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Inositol 1,4,5-trisphosphate receptor type 1 / IP3 receptor isoform 1 / InsP3R1 / Inositol 1 / 4 / 5-trisphosphate-binding protein P400 / Protein ...IP3 receptor isoform 1 / InsP3R1 / Inositol 1 / 4 / 5-trisphosphate-binding protein P400 / Protein PCD-6 / Purkinje cell protein 1 / Type 1 inositol 1 / 5-trisphosphate receptor / Type 1 InsP3 receptor


Mass: 252377.312 Da / Num. of mol.: 2 / Fragment: UNP residues 1-2217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itpr1, Insp3r, Pcd6, Pcp1 / Production host: Spodoptera (butterflies/moths) / References: UniProt: P11881

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.3→49.1 Å / Num. obs: 10669 / % possible obs: 99.86 % / Redundancy: 11.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.5
Reflection shellResolution: 7.311→7.572 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.5745 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 1030 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fragments of 3JAV C-alpha model and 3UJ4 chain A

3jav

3uj4


Resolution: 7.311→49.145 Å / SU ML: 1.71 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 45.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3937 536 5.02 %
Rwork0.317 --
obs0.3209 10669 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7.311→49.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16948 0 0 0 16948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916920
X-RAY DIFFRACTIONf_angle_d1.45223558
X-RAY DIFFRACTIONf_dihedral_angle_d6.3149942
X-RAY DIFFRACTIONf_chiral_restr0.0583276
X-RAY DIFFRACTIONf_plane_restr0.0083390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.3114-8.04430.41031320.33142487X-RAY DIFFRACTION99
8.0443-9.20170.38141310.31782483X-RAY DIFFRACTION100
9.2017-11.56820.3341340.28762535X-RAY DIFFRACTION100
11.5682-49.14660.43211390.33052628X-RAY DIFFRACTION100

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