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

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Basic information

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


cGMP effects / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / smooth endoplasmic reticulum membrane / platelet dense tubular network / negative regulation of calcium-mediated signaling / calcineurin complex / platelet dense granule membrane / epithelial fluid transport ...cGMP effects / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / smooth endoplasmic reticulum membrane / platelet dense tubular network / negative regulation of calcium-mediated signaling / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / inositol 1,4,5-trisphosphate-gated calcium channel activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / voluntary musculoskeletal movement / Ion homeostasis / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / 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 / GABA-ergic synapse / calcium channel inhibitor activity / release of sequestered calcium ion into cytosol / cellular response to cAMP / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / synaptic membrane / sarcoplasmic reticulum / liver regeneration / Schaffer collateral - CA1 synapse / cell morphogenesis / positive regulation of insulin secretion / positive regulation of neuron projection development / calcium ion transport / presynapse / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / postsynapse / protein phosphatase binding / transmembrane transporter binding / postsynaptic density / response to hypoxia / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / synapse / calcium ion binding / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / identical protein binding / 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 / 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
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol 1,4,5-trisphosphate-gated calcium channel ITPR1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 7.399 Å
AuthorsHamada, K. / Miyatake, H. / Terauchi, A. / Mikoshiba, K.
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
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,5954
Polymers504,7552
Non-polymers8402
Water00
1
A: Inositol 1,4,5-trisphosphate receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,7972
Polymers252,3771
Non-polymers4201
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-6 kcal/mol
Surface area99840 Å2
MethodPISA
2
B: Inositol 1,4,5-trisphosphate receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,7972
Polymers252,3771
Non-polymers4201
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area101620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.988, 223.488, 319.869
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 frugiperda (fall armyworm) / References: UniProt: P11881
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H15O15P3

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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: 3.75 Å3/Da / Density % sol: 67.17 %
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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.399→49.49 Å / Num. obs: 10397 / % possible obs: 99.4 % / Redundancy: 10.7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.294 / Net I/σ(I): 6.94
Reflection shellResolution: 7.399→7.663 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.5721 / Mean I/σ(I) obs: 2.17 / CC1/2: 0.258 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSVERSION May 1, 2016data reduction
XDSVERSION May 1, 2016data scaling
PHASER2.6.0phasing
RefinementResolution: 7.399→49.489 Å / SU ML: 2.15 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 52.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4159 526 5.06 %
Rwork0.3563 --
obs0.3594 10397 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7.399→49.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17259 0 48 0 17307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01517277
X-RAY DIFFRACTIONf_angle_d1.69324027
X-RAY DIFFRACTIONf_dihedral_angle_d5.89610171
X-RAY DIFFRACTIONf_chiral_restr0.0563325
X-RAY DIFFRACTIONf_plane_restr0.0093435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.3988-8.14040.4091340.37792414X-RAY DIFFRACTION100
8.1404-9.31150.39661280.35852433X-RAY DIFFRACTION100
9.3115-11.70580.35851290.31412469X-RAY DIFFRACTION100
11.7058-49.49010.47261350.37582555X-RAY DIFFRACTION100

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