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- PDB-1xzz: Crystal structure of the ligand binding suppressor domain of type... -

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Basic information

Entry
Database: PDB / ID: 1xzz
TitleCrystal structure of the ligand binding suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsMEMBRANE PROTEIN / IP3 RECEPTOR / IP3 RECEPTOR SUPPRESSOR DOMAIN / CALCIUM CHANNEL / B-TREFOIL 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
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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Ion transport domain / Ion transport protein / Mainly Beta
Similarity search - Domain/homology
Inositol 1,4,5-trisphosphate receptor type 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsBosanac, I. / Yamazaki, H. / Matsu-ura, T. / Michikawa, T. / Mikoshiba, K. / Ikura, M.
CitationJournal: Mol.Cell / Year: 2005
Title: Crystal structure of the ligand binding suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor.
Authors: Bosanac, I. / Yamazaki, H. / Matsu-Ura, T. / Michikawa, T. / Mikoshiba, K. / Ikura, M.
History
DepositionNov 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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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)27,5132
Polymers27,4211
Non-polymers921
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.300, 147.300, 65.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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 / Protein PCD-6


Mass: 27421.232 Da / Num. of mol.: 1 / Fragment: IP3R suppressor domain (residues 2-223)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itpr1, Insp3r, Pcd6, Pcp1 / Plasmid: pET-23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-CodonPlus(DE3) / References: UniProt: P11881
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Tris-HCl, PEG 6000, NaCl, TCEP, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.9951
SYNCHROTRONAPS 19-BM20.9795, 0.9796, 0.9641
Detector
TypeIDDetectorDateDetails
APS-11CCDMar 5, 2003Rosenbaum-Rock double-crystal monochromator: water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
APS-12CCDMar 5, 2003Rosenbaum-Rock double-crystal monochromator: water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock double-crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.99511
20.97951
30.97961
40.96411
ReflectionResolution: 1.64→50 Å / Num. obs: 32835 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 75
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 7 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3151 / % possible all: 96.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→31.08 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1185381.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1187 4.9 %RANDOM
Rwork0.205 ---
obs0.205 24349 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9874 Å2 / ksol: 0.361298 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20.32 Å20 Å2
2---0.68 Å20 Å2
3---1.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 6 130 1841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it3.551.5
X-RAY DIFFRACTIONc_mcangle_it4.512
X-RAY DIFFRACTIONc_scbond_it5.622
X-RAY DIFFRACTIONc_scangle_it7.562.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 185 4.8 %
Rwork0.22 3636 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CRY_XPLOR_PAR.TXTCRY_XPLOR_TOP.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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