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- PDB-3t8s: Apo and InsP3-bound Crystal Structures of the Ligand-Binding Doma... -

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Basic information

Entry
Database: PDB / ID: 3t8s
TitleApo and InsP3-bound Crystal Structures of the Ligand-Binding Domain of an InsP3 Receptor
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsTransport protein / membrane protein / Beta-trefoil fold / armadillo repeat fold / ligand-binding domain / ligand(IP3)-binding / IP3 / Endoplasmic reticulum / ligand gated channel / Ca2+ release channel
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 ...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 / platelet dense granule membrane / calcineurin complex / 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-sensitive calcium-release channel activity / 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 / release of sequestered calcium ion into cytosol / cellular response to cAMP / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / synaptic membrane / sarcoplasmic reticulum / liver regeneration / Schaffer collateral - CA1 synapse / cytoplasmic vesicle membrane / 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 / membrane raft / protein domain specific binding / intracellular membrane-bounded organelle / neuronal cell body / dendrite / 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 / Inositol 1,4,5-trisphosphate receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.77 Å
AuthorsLin, C. / Baek, K. / Lu, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Apo and InsP(3)-bound crystal structures of the ligand-binding domain of an InsP(3) receptor.
Authors: Lin, C.C. / Baek, K. / Lu, Z.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_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_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

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)132,6123
Polymers132,1922
Non-polymers4201
Water0
1
A: Inositol 1,4,5-trisphosphate receptor type 1


Theoretical massNumber of molelcules
Total (without water)66,0961
Polymers66,0961
Non-polymers00
Water0
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)66,5162
Polymers66,0961
Non-polymers4201
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.829, 84.877, 95.090
Angle α, β, γ (deg.)90.00, 116.92, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 7 - 580 / Label seq-ID: 5 - 563

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein Inositol 1,4,5-trisphosphate receptor type 1 / IP3 receptor isoform 1 / IP-3-R / IP3R 1 / InsP3R1 / Type 1 inositol 1 / 4 / 5-trisphosphate ...IP3 receptor isoform 1 / IP-3-R / IP3R 1 / InsP3R1 / Type 1 inositol 1 / 4 / 5-trisphosphate receptor / Type 1 InsP3 receptor


Mass: 66095.953 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Insp3r, Itpr1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29994-2, UniProt: P29994*PLUS
#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

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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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100 mM 2-(N-morpholino)ethanesulfonic acid, 4.5% PEG 3350, 0.1 M sodium formate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.75→50 Å / Num. all: 11524 / Num. obs: 11512 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.75-3.883.60.783199.6
3.88-4.043.70.701199.9
4.04-4.223.80.3931100
4.22-4.453.80.2611100
4.45-4.723.80.1881100
4.72-5.093.80.16199.9
5.09-5.63.80.1421100
5.6-6.413.80.1211100
6.41-8.073.80.0691100
8.07-503.60.038199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.77 Å42.39 Å
Translation3.77 Å42.39 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1N4K, 1XZZ
Resolution: 3.77→41.45 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0 / SU B: 185.426 / SU ML: 1.146 / SU R Cruickshank DPI: 0.8821 / Cross valid method: THROUGHOUT / ESU R Free: 0.92 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29165 540 4.7 %RANDOM
Rwork0.27731 ---
obs0.27805 10936 99.07 %-
all-11584 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.853 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.08 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.77→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 24 0 7386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.94910222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42424.969326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.312151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5281531
X-RAY DIFFRACTIONr_chiral_restr0.0740.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215679
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 3452 / Type: medium positional / Rms dev position: 0.68 Å / Weight position: 0.5
LS refinement shellResolution: 3.77→3.868 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 28 -
Rwork0.373 732 -
obs--91.57 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.12820.11760.04551.63442.27153.22220.29070.2091-0.22910.0045-0.1716-0.07190.01160.3874-0.11910.32020.14320.02410.45090.01230.3461-0.992248.878934.8269
20.45280.08681.26430.9559-1.2225.02130.08570.0742-0.26250.3034-0.0591-0.4002-0.02520.3088-0.02660.453-0.0991-0.10190.1028-0.11190.5228-30.780312.84195.8777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 580
2X-RAY DIFFRACTION2B7 - 580

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