[English] 日本語
Yorodumi
- PDB-3ila: Crystal structure of rabbit ryanodine receptor 1 N-terminal domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ila
TitleCrystal structure of rabbit ryanodine receptor 1 N-terminal domain (9-205)
ComponentsRyanodine receptor 1
KeywordsSIGNALING PROTEIN / BETA TREFOIL / Calcium channel / Calcium transport / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Receptor / S-nitrosylation / Transmembrane / Transport
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein binding
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 / 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 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLobo, P.A. / Van Petegem, F.
CitationJournal: Structure / Year: 2009
Title: Crystal structures of the N-terminal domains of cardiac and skeletal muscle ryanodine receptors: insights into disease mutations.
Authors: Lobo, P.A. / Van Petegem, F.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ryanodine receptor 1
B: Ryanodine receptor 1
C: Ryanodine receptor 1
D: Ryanodine receptor 1
E: Ryanodine receptor 1
F: Ryanodine receptor 1
G: Ryanodine receptor 1
H: Ryanodine receptor 1
I: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)195,9459
Polymers195,9459
Non-polymers00
Water0
1
A: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)21,7721
Polymers21,7721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.734, 155.705, 81.613
Angle α, β, γ (deg.)90.00, 110.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ryanodine receptor 1 / / RYR-1 / RyR1 / Skeletal muscle-type ryanodine receptor / Skeletal muscle calcium release channel


Mass: 21771.654 Da / Num. of mol.: 9 / Fragment: N-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Plasmid: pET28 HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 placI / References: UniProt: P11716

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-25% PEG 3350, 0.2M sodium chloride, 0.1M BisTris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2008 / Details: Double Crystal Monochromator, mirrors
RadiationMonochromator: Double Crystal Monochromator with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 36063 / Num. obs: 32354 / % possible obs: 69.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 59.146 Å2 / Rsym value: 0.14 / Net I/σ(I): 13.28
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.33 / Num. unique all: 1837 / Rsym value: 0.416 / % possible all: 45.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ryanodine Receptor isoform 2

Resolution: 2.9→48.51 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.823 / SU B: 52.997 / SU ML: 0.481 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31991 1736 5.1 %RANDOM
Rwork0.27413 ---
all0.27653 34226 --
obs0.27653 28582 93.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.983 Å2
Baniso -1Baniso -2Baniso -3
1-6.53 Å20 Å2-0.08 Å2
2---3.67 Å20 Å2
3----2.91 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9944 0 0 0 9944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02110079
X-RAY DIFFRACTIONr_angle_refined_deg0.7841.9613697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.98251326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31723.894339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.061151393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0111534
X-RAY DIFFRACTIONr_chiral_restr0.0460.21710
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.027291
X-RAY DIFFRACTIONr_nbd_refined0.1320.23344
X-RAY DIFFRACTIONr_nbtor_refined0.2780.26571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.25
X-RAY DIFFRACTIONr_mcbond_it0.1241.57056
X-RAY DIFFRACTIONr_mcangle_it0.225210665
X-RAY DIFFRACTIONr_scbond_it0.16533505
X-RAY DIFFRACTIONr_scangle_it0.2634.53032
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 89 -
Rwork0.293 1710 -
obs--67.4 %
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)
12.0740.1118-1.00043.545-1.06894.4058-0.0170.04560.12710.1542-0.0460.1891-0.2102-0.0220.063-0.40230.0166-0.0385-0.2792-0.0339-0.2861-11.00248.363623.4148
23.25170.3623-0.90962.7835-1.44054.2586-0.08860.0726-0.2250.01070.1095-0.1705-0.34320.1833-0.0209-0.3917-0.06190.019-0.26-0.061-0.307220.43955.74581.7602
32.05680.70930.31554.66682.07485.4032-0.0149-0.0380.00450.0824-0.10160.22880.2251-0.27720.1165-0.4326-0.0478-0.0397-0.27270.0184-0.353-19.1337-16.61211.407
42.225-0.82830.3716.9187-1.94083.8966-0.03510.0114-0.0994-0.0429-0.09-0.0519-0.0865-0.0050.1251-0.3244-0.02170.0617-0.38420.0025-0.3554-19.8068-42.600425.0199
51.62880.020.46533.43390.9723.73490.0813-0.0213-0.00130.1307-0.087-0.05760.18560.05770.0057-0.3325-0.06920.0076-0.28630.0439-0.366-13.1427-20.304149.6144
61.58950.5098-0.334.6959-1.0163.39450.0603-0.01730.0717-0.0361-0.06770.1128-0.0986-0.11580.0074-0.37590.00560.0009-0.32140.0149-0.351122.229310.469249.8009
71.7090.6666-0.33475.35730.12463.63440.0718-0.0550.12320.1608-0.07110.02020.432-0.1651-0.0007-0.2940.0009-0.0549-0.3461-0.0026-0.41217.5126-45.079352.2736
82.8066-0.80761.01693.5887-0.89743.47820.056-0.0508-0.17430.0230.27240.40050.00090.0047-0.3284-0.43840.05030.0417-0.32410.1185-0.221416.5457-18.690324.5892
93.32430.55160.11373.9852-1.96793.6209-0.0639-0.06510.5505-1.0366-0.14920.31230.39470.39230.2131-0.49020.0744-0.0376-0.41360.0649-0.280519.2363-44.19046.5785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C1 - 205
4X-RAY DIFFRACTION4D1 - 205
5X-RAY DIFFRACTION5E1 - 205
6X-RAY DIFFRACTION6F1 - 205
7X-RAY DIFFRACTION7G1 - 205
8X-RAY DIFFRACTION8H1 - 205
9X-RAY DIFFRACTION9I1 - 205

+
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