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- PDB-3uj4: Crystal structure of the apo-inositol 1,4,5-trisphosphate receptor -

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Basic information

Entry
Database: PDB / ID: 3uj4
TitleCrystal structure of the apo-inositol 1,4,5-trisphosphate receptor
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsSIGNALING PROTEIN / inositol 1 / 4 / 5-trisphosphate / apo-state / suppressor domain / IP3-binding core domain
Function / homology
Function and homology information


Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / negative regulation of calcium-mediated signaling / calcineurin complex / platelet dense granule membrane ...Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / Elevation of cytosolic Ca2+ levels / cGMP effects / 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 / regulation of postsynaptic cytosolic calcium ion concentration / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / nuclear inner membrane / transport vesicle membrane / Ion homeostasis / dendrite development / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / GABA-ergic synapse / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / calcium channel inhibitor activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / sarcoplasmic reticulum / synaptic membrane / liver regeneration / calcium-mediated signaling / calcium ion transmembrane transport / Schaffer collateral - CA1 synapse / cell morphogenesis / positive regulation of neuron projection development / positive regulation of insulin secretion / calcium ion transport / presynapse / nuclear envelope / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cellular response to hypoxia / postsynapse / protein phosphatase binding / transmembrane transporter binding / postsynaptic density / response to hypoxia / positive regulation of apoptotic process / protein domain specific binding / dendrite / neuronal cell body / synapse / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
IP3 receptor type 1 binding core, RIH domain / 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 ...IP3 receptor type 1 binding core, RIH domain / 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 / Leucine-rich Repeat Variant / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Ion transport domain / Ion transport protein / Alpha Horseshoe / Armadillo-type fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Inositol 1,4,5-trisphosphate receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsIkura, M. / Seo, M.D. / Ishiyama, N. / Stathopulos, P.
CitationJournal: Nature / Year: 2012
Title: Structural and functional conservation of key domains in InsP3 and ryanodine receptors.
Authors: Seo, M.D. / Velamakanni, S. / Ishiyama, N. / Stathopulos, P.B. / Rossi, A.M. / Khan, S.A. / Dale, P. / Li, C. / Ames, J.B. / Ikura, M. / Taylor, C.W.
History
DepositionNov 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)136,0803
Polymers135,9832
Non-polymers961
Water50428
1
A: Inositol 1,4,5-trisphosphate receptor type 1


Theoretical massNumber of molelcules
Total (without water)67,9921
Polymers67,9921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inositol 1,4,5-trisphosphate receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0882
Polymers67,9921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.108, 77.191, 101.509
Angle α, β, γ (deg.)105.360, 99.980, 101.040
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Inositol 1,4,5-trisphosphate receptor type 1 / IP-3-R / IP3R 1 / InsP3R1 / Type 1 inositol 1 / 4 / 5-trisphosphate receptor / Type 1 InsP3 receptor


Mass: 67991.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Itpr1, Insp3r / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: P29994
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1 M Hepes, (NH4)2SO4), trimethylamine N-oxide, pH 8.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 133458

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.007 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 1746 5 %RANDOM
Rwork0.2084 ---
obs0.2108 34787 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.28 Å2 / Biso mean: 87.7 Å2 / Biso min: 19.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-3.12 Å21.93 Å2
2---0.35 Å20.31 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7421 0 5 28 7454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027569
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.94910288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58224.509326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.362151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4551536
X-RAY DIFFRACTIONr_chiral_restr0.0760.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215694
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 110 -
Rwork0.259 2429 -
all-2539 -
obs--98.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.19820.2078-0.50753.867-1.47663.01960.0630.28580.2231-0.065-0.1145-0.2599-0.00980.12920.05150.0105-0.02090.03320.1434-0.0230.2347-8.209-24.28231.102
25.6887-0.25150.13994.7277-0.1274.38320.15070.78470.3045-0.40890.03170.1666-0.1861-0.1657-0.18240.05430.04690.0420.3840.06280.3642-36.997-9.58119.081
34.3298-0.1975-4.637910.9144-5.620416.15310.00410.62280.1094-1.6068-0.4117-0.88860.18521.65450.40760.44550.08990.17570.94820.09530.2603-10.192-15.0482.629
42.18560.57290.34136.9153-2.90125.19150.1168-0.2938-0.28120.2226-0.4055-0.80660.63610.44710.28870.2413-0.01740.00410.18860.02760.3361-6.989-49.81849.507
54.46951.30240.07856.36310.55066.7130.1619-0.2863-0.09350.6586-0.17020.4420.256-0.22340.00830.1563-0.07220.0920.1368-0.00970.4091-30.405-75.50948.991
61.23952.10121.31867.5484-2.70129.84150.1983-0.4455-0.00091.1262-0.2624-0.1359-0.27170.23050.06411.06760.00840.11211.13870.00150.3211-18.416-61.43174.874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 228
2X-RAY DIFFRACTION2A229 - 435
3X-RAY DIFFRACTION3A436 - 577
4X-RAY DIFFRACTION4B7 - 228
5X-RAY DIFFRACTION5B229 - 435
6X-RAY DIFFRACTION6B436 - 577

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