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- PDB-3jrr: Crystal structure of the ligand binding suppressor domain of type... -

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Basic information

Entry
Database: PDB / ID: 3jrr
TitleCrystal structure of the ligand binding suppressor domain of type 3 inositol 1,4,5-trisphosphate receptor
ComponentsInositol 1,4,5-trisphosphate receptor type 3
KeywordsTRANSPORT PROTEIN / beta-trefoil / Calcium channel / Calcium transport / Endoplasmic reticulum / Ion transport / Ionic channel / Membrane / Phosphoprotein / Receptor / Transmembrane / Transport
Function / homology
Function and homology information


Effects of PIP2 hydrolysis / Sensory perception of sweet, bitter, and umami (glutamate) taste / Elevation of cytosolic Ca2+ levels / sensory perception of bitter taste / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of umami taste / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / sensory perception of sweet taste / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / inositol 1,4,5 trisphosphate binding ...Effects of PIP2 hydrolysis / Sensory perception of sweet, bitter, and umami (glutamate) taste / Elevation of cytosolic Ca2+ levels / sensory perception of bitter taste / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of umami taste / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / sensory perception of sweet taste / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / inositol 1,4,5 trisphosphate binding / Ion homeostasis / transport vesicle membrane / cytoplasmic side of endoplasmic reticulum membrane / intracellularly gated calcium channel activity / calcium ion homeostasis / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / platelet activation / memory / long-term synaptic potentiation / response to calcium ion / calcium ion transport / protein homotetramerization / receptor complex / calcium ion binding / nucleolus / zinc ion binding / nucleoplasm / ATP binding / nucleus / 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-gated calcium channel ITPR3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsChan, J. / Ishiyama, N. / Ikura, M.
CitationJournal: To be Published
Title: A 1.9 angstrom crystal structure of the suppressor domain of type 3 inositol 1,4,5-trisphosphate receptor
Authors: Chan, J. / Yamazaki, H. / Ishiyama, N. / Mal, T.K. / Michikawa, T. / Mikoshiba, K. / Ikura, M.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 3
B: Inositol 1,4,5-trisphosphate receptor type 3


Theoretical massNumber of molelcules
Total (without water)50,6682
Polymers50,6682
Non-polymers00
Water3,621201
1
A: Inositol 1,4,5-trisphosphate receptor type 3


Theoretical massNumber of molelcules
Total (without water)25,3341
Polymers25,3341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inositol 1,4,5-trisphosphate receptor type 3


Theoretical massNumber of molelcules
Total (without water)25,3341
Polymers25,3341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.441, 59.865, 111.399
Angle α, β, γ (deg.)90.000, 97.877, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Inositol 1,4,5-trisphosphate receptor type 3 / Type 3 inositol 1 / 4 / 5-trisphosphate receptor / Type 3 InsP3 receptor / IP3 receptor isoform 3 / InsP3R3


Mass: 25333.953 Da / Num. of mol.: 2 / Fragment: UNP residues 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itpr3 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70227
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1M HEPES, 0.15M NaCl, 14% PEG 4000, 2mM TCEP, 1% Dioxane, 50mM EDTA , pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 15, 2007 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 40451 / Num. obs: 40370 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 14 Å2 / Limit h max: 41 / Limit h min: -41 / Limit k max: 31 / Limit k min: -41 / Limit l max: 58 / Limit l min: 0 / Observed criterion F max: 155781.3 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Num. unique all: 4004 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.585 / Packing: 0.538
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral98.6 0

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XZZ

1xzz


Resolution: 1.9→50 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3853 10 %random
Rwork0.214 ---
all-40934 --
obs-38649 94.4 %-
Solvent computationSolvent model: bulk solvent model / Bsol: 33.3111 Å2 / ksol: 0.361486 e/Å3
Displacement parametersBiso max: 59.66 Å2 / Biso mean: 25.26 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20.71 Å2
2---0.02 Å20 Å2
3---1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-7 Å
Luzzati sigma a0.15 Å0.12 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 0 201 3623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.67
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.28844810.80.24436830.0145135413180.4
1.99-2.090.2454409.30.21642740.0125063471493.1
2.09-2.220.2514789.90.21243640.0115078484295.4
2.22-2.40.2454779.80.21143960.0115113487395.3
2.4-2.640.2744779.70.24144410.0135091491896.6
2.64-3.020.27850410.10.23744750.0125114497997.4
3.02-3.80.2594949.70.21445770.0125154507198.4
3.8-30.360.21353510.40.19145860.0095228512197.9

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