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- PDB-3uj0: Crystal structure of the inositol 1,4,5-trisphosphate receptor wi... -

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Basic information

Entry
Database: PDB / ID: 3uj0
TitleCrystal structure of the inositol 1,4,5-trisphosphate receptor with ligand bound form.
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsSIGNALING PROTEIN / inositol 1 / 4 / 5-trisphosphate / IP3-bound form / 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
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol 1,4,5-trisphosphate receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)136,8244
Polymers135,9832
Non-polymers8402
Water1629
1
A: Inositol 1,4,5-trisphosphate receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4122
Polymers67,9921
Non-polymers4201
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)68,4122
Polymers67,9921
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)189.166, 78.720, 134.107
Angle α, β, γ (deg.)90.000, 124.490, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASP1AA7 - 2287 - 228
21SERSERASPASP1BB7 - 2287 - 228
12LYSLYSVALVAL1AA230 - 435230 - 435
22LYSLYSVALVAL1BB230 - 435230 - 435
13SERSERILEILE4AA436 - 585436 - 585
23SERSERILEILE4BB436 - 585436 - 585

NCS ensembles :
ID
1
2
3

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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-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: Na Citrate, PEG-6000, 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-BM
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 71417

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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: 3.6→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / SU B: 93.143 / SU ML: 0.647 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.741 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3078 982 5.2 %RANDOM
Rwork0.2575 ---
obs0.26 19043 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.52 Å2 / Biso mean: 133.186 Å2 / Biso min: 28.76 Å2
Baniso -1Baniso -2Baniso -3
1--10.81 Å20 Å2-0.16 Å2
2--9.2 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7722 0 48 9 7779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027911
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.95610723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15724.729351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.971151319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5921540
X-RAY DIFFRACTIONr_chiral_restr0.0720.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215889
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11661TIGHT THERMAL3.330.5
21215TIGHT THERMAL5.30.5
3960MEDIUM POSITIONAL0.310.5
3960MEDIUM THERMAL13.512
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 75 -
Rwork0.371 1240 -
all-1315 -
obs--99.55 %
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)
13.0295-0.12841.28092.2962-0.64551.70960.2082-0.1048-0.2871-0.0161-0.0026-0.10430.15110.1452-0.20561.025-0.05190.07060.0421-0.03440.530618.733-10.48326.539
22.939-0.2935-1.19522.1160.65911.28940.0781-0.1280.1477-0.04040.05640.0853-0.1203-0.0375-0.13450.9582-0.00330.03870.02680.05760.483-18.11534.94226.38
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 228
2X-RAY DIFFRACTION1A229 - 435
3X-RAY DIFFRACTION1A436 - 585
4X-RAY DIFFRACTION2B7 - 228
5X-RAY DIFFRACTION2B229 - 435
6X-RAY DIFFRACTION2B436 - 577

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