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- PDB-1n4k: Crystal structure of the inositol 1,4,5-trisphosphate receptor bi... -

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Basic information

Entry
Database: PDB / ID: 1n4k
TitleCrystal structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with IP3
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsMEMBRANE PROTEIN / IP3 RECEPTOR / IP3-BINDING CORE / CALCIUM CHANNEL / PROTEIN-LIGAND COMPLEX / B-TREFOIL FOLD / ARMADILLO-LIKE FOLD
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 / 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 / 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 / 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 / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol 1,4,5-trisphosphate receptor type 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsBosanac, I. / Alattia, J.R. / Mal, T.K. / Chan, J. / Talarico, S. / Tong, F.K. / Tong, K.I. / Yoshikawa, F. / Furuichi, T. / Iwai, M. ...Bosanac, I. / Alattia, J.R. / Mal, T.K. / Chan, J. / Talarico, S. / Tong, F.K. / Tong, K.I. / Yoshikawa, F. / Furuichi, T. / Iwai, M. / Michikawa, T. / Mikoshiba, K. / Ikura, M.
CitationJournal: Nature / Year: 2002
Title: Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand.
Authors: Bosanac, I. / Alattia, J.R. / Mal, T.K. / Chan, J. / Talarico, S. / Tong, F.K. / Tong, K.I. / Yoshikawa, F. / Furuichi, T. / Iwai, M. / Michikawa, T. / Mikoshiba, K. / Ikura, M.
History
DepositionOct 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0232
Polymers43,6031
Non-polymers4201
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.101, 90.420, 207.117
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 / Type 1 inositol 1 / 4 / 5- trisphosphate receptor / Type 1 InsP3 receptor / IP3 receptor isoform 1 ...Type 1 inositol 1 / 4 / 5- trisphosphate receptor / Type 1 InsP3 receptor / IP3 receptor isoform 1 / InsP3R1 / Inositol 1 / 4 / 5-trisphosphate-binding protein P400 / Purkinje cell protein 1


Mass: 43603.270 Da / Num. of mol.: 1 / Fragment: IP3-binding core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ITPR1 OR INSP3R / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-CodonPlus(DE3) / References: UniProt: P11881
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, PEG 3350, ammonium formate, TCEP, dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
215 mMTris-HCl1droppH8.0
3300 mM1dropNa2SO4
42 mMTris(2-carboxyethyl)phosphine1drop
550 %InsP31dropmolar excess
6100 mMMES1reservoirpH6.0
720 %PEG33501reservoir
80.2 M1reservoirCH5NO3
92-5 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.95 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Nov 12, 2001
RadiationMonochromator: rotated-inclined double crystal as a monochrometer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→37.82 Å / Num. all: 21569 / Num. obs: 20991 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 8.4 / % possible all: 80.8
Reflection
*PLUS
Lowest resolution: 42 Å / Num. measured all: 136748
Reflection shell
*PLUS
% possible obs: 80.8 %

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Processing

Software
NameClassification
d*TREKdata scaling
d*TREKdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→37.82 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2424922.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2060 9.8 %RANDOM
Rwork0.224 ---
obs0.224 20935 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0907 Å2 / ksol: 0.36677 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--0.99 Å20 Å2
3----2.04 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 24 140 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 281 9.3 %
Rwork0.226 2745 -
obs-3026 86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2I3P_XPLOR_PAR.TXTI3P_XPLOR_TOP.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.066
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63

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