[English] 日本語
Yorodumi
- PDB-3jrr: Crystal structure of the ligand binding suppressor domain of type... -

+
Open data


ID or keywords:

Loading...

-
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


Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / : / sensory perception of bitter taste / sensory perception of umami taste / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of sweet taste / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion ...Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / : / sensory perception of bitter taste / sensory perception of umami taste / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of sweet taste / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / inositol hexakisphosphate binding / Ion homeostasis / inositol 1,4,5 trisphosphate binding / nuclear outer membrane / calcium ion transport into cytosol / intracellularly gated calcium channel activity / plasma membrane => GO:0005886 / brush border / cellular response to cAMP / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / secretory granule membrane / sarcoplasmic reticulum / long-term synaptic potentiation / cytoplasmic vesicle membrane / memory / response to calcium ion / calcium ion transport / presynapse / apical part of cell / myelin sheath / nuclear envelope / positive regulation of cytosolic calcium ion concentration / receptor complex / G protein-coupled receptor signaling pathway / dendrite / neuronal cell body / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / nucleoplasm / identical protein 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 / MIR 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 / 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 3
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more