[English] 日本語
Yorodumi
- PDB-4kej: Crystal structure of mouse Ryanodine Receptor 2 (1-217) disease m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kej
TitleCrystal structure of mouse Ryanodine Receptor 2 (1-217) disease mutant R169Q
ComponentsRyanodine receptor 2
KeywordsMETAL TRANSPORT / Ca2+ release / ion channel / ER/SR Membrane
Function / homology
Function and homology information


manganese ion transmembrane transport / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential ...manganese ion transmembrane transport / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / Stimuli-sensing channels / Ion homeostasis / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / calcium ion transport into cytosol / calcium ion transmembrane import into cytosol / response to caffeine / A band / response to redox state / positive regulation of heart rate / negative regulation of cytosolic calcium ion concentration / cellular response to caffeine / protein kinase A regulatory subunit binding / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / response to magnesium ion / : / detection of calcium ion / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / monoatomic ion transmembrane transport / extrinsic component of cytoplasmic side of plasma membrane / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / response to muscle stretch / regulation of heart rate / sarcomere / sarcoplasmic reticulum / establishment of localization in cell / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / response to calcium ion / calcium ion transport / : / nuclear envelope / scaffold protein binding / calmodulin binding / response to hypoxia / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein binding / membrane
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / 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 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ryanodine receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 Å
AuthorsKimlicka, L. / Van Petegem, F.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Type 2 Ryanodine Receptor Domain A Contains a Unique and Dynamic alpha-Helix That Transitions to a beta-Strand in a Mutant Linked with a Heritable Cardiomyopathy.
Authors: Amador, F.J. / Kimlicka, L. / Stathopulos, P.B. / Gasmi-Seabrook, G.M. / Maclennan, D.H. / Van Petegem, F. / Ikura, M.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Sep 20, 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: Ryanodine receptor 2


Theoretical massNumber of molelcules
Total (without water)24,1381
Polymers24,1381
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.859, 112.859, 38.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Ryanodine receptor 2 / RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium ...RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor / Cardiac Ca2+ release channel


Mass: 24138.137 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-217) / Mutation: R169Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: E9Q401
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M sodium malonate, 5-15% saturated ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 8011 / Num. obs: 7914 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.55-2.64190
2.64-2.75197.9
2.75-2.871100
2.87-3.021100
3.02-3.211100
3.21-3.461100
3.46-3.811100
3.81-4.361100
4.36-5.491100
5.49-50199.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IM7

3im7


Resolution: 2.553→39.902 Å / SU ML: 0.35 / σ(F): 0.09 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2967 347 4.64 %RANDOM
Rwork0.2357 ---
obs0.2385 7484 93.5 %-
all-8011 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.236 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0478 Å20 Å20 Å2
2---0.0478 Å20 Å2
3---0.0957 Å2
Refinement stepCycle: LAST / Resolution: 2.553→39.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 0 19 1277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031287
X-RAY DIFFRACTIONf_angle_d0.6961758
X-RAY DIFFRACTIONf_dihedral_angle_d14.753415
X-RAY DIFFRACTIONf_chiral_restr0.044215
X-RAY DIFFRACTIONf_plane_restr0.002220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.553-3.21670.33081640.25253333X-RAY DIFFRACTION88
3.2167-39.90650.28131830.22943804X-RAY DIFFRACTION98

+
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://pdbjlvh1.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