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- PDB-6j6l: Crystal structure of mouse Ryanodine Receptor 2 SPRY1 Domain (650... -

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Basic information

Entry
Database: PDB / ID: 6j6l
TitleCrystal structure of mouse Ryanodine Receptor 2 SPRY1 Domain (650-844) disease mutant I784F
ComponentsRyanodine receptor 2
KeywordsMETAL TRANSPORT / Ryanodine Receptor 2 / SPRY1 / disease mutation
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential / regulation of SA node cell action potential / : / Stimuli-sensing channels ...establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential / regulation of SA node cell action potential / : / Stimuli-sensing channels / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / Ion homeostasis / positive regulation of sequestering of calcium ion / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / response to caffeine / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / calcium ion transmembrane import into cytosol / response to muscle activity / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / cellular response to caffeine / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / detection of calcium ion / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / smooth endoplasmic reticulum / positive regulation of heart rate / response to muscle stretch / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / calcium channel complex / regulation of heart rate / sarcoplasmic reticulum / sarcomere / establishment of localization in cell / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / Z disc / intracellular calcium ion homeostasis / calcium ion transport / response to hypoxia / calmodulin binding / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein binding / membrane
Similarity search - Function
SPRY domain / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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 ...SPRY domain / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Ryanodine receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.452 Å
AuthorsMa, R. / Lin, L. / Yuchi, Z.
CitationJournal: Sci Rep / Year: 2021
Title: A SPRY1 domain cardiac ryanodine receptor variant associated with short-coupled torsade de pointes.
Authors: Touat-Hamici, Z. / Blancard, M. / Ma, R. / Lin, L. / Iddir, Y. / Denjoy, I. / Leenhardt, A. / Yuchi, Z. / Guicheney, P.
History
DepositionJan 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 2
B: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4588
Polymers44,0972
Non-polymers3616
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint8 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.945, 64.375, 108.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 652 through 654 or resid 656...
21(chain B and (resid 652 through 654 or resid 656...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER(chain A and (resid 652 through 654 or resid 656...AA652 - 6546 - 8
12ARGARGASNASN(chain A and (resid 652 through 654 or resid 656...AA656 - 65810 - 12
13PHEPHESERSER(chain A and (resid 652 through 654 or resid 656...AA660 - 66414 - 18
14GLUGLUGLUGLU(chain A and (resid 652 through 654 or resid 656...AA66519
15HISHISTYRTYR(chain A and (resid 652 through 654 or resid 656...AA651 - 8405 - 194
16HISHISTYRTYR(chain A and (resid 652 through 654 or resid 656...AA651 - 8405 - 194
17HISHISTYRTYR(chain A and (resid 652 through 654 or resid 656...AA651 - 8405 - 194
18HISHISTYRTYR(chain A and (resid 652 through 654 or resid 656...AA651 - 8405 - 194
21VALVALSERSER(chain B and (resid 652 through 654 or resid 656...BB652 - 6546 - 8
22ARGARGASNASN(chain B and (resid 652 through 654 or resid 656...BB656 - 65810 - 12
23PHEPHEGLNGLN(chain B and (resid 652 through 654 or resid 656...BB660 - 66914 - 23
24VALVALTYRTYR(chain B and (resid 652 through 654 or resid 656...BB652 - 8406 - 194
25VALVALTYRTYR(chain B and (resid 652 through 654 or resid 656...BB652 - 8406 - 194
26VALVALTYRTYR(chain B and (resid 652 through 654 or resid 656...BB652 - 8406 - 194
27VALVALTYRTYR(chain B and (resid 652 through 654 or resid 656...BB652 - 8406 - 194
28VALVALTYRTYR(chain B and (resid 652 through 654 or resid 656...BB652 - 8406 - 194
29VALVALTYRTYR(chain B and (resid 652 through 654 or resid 656...BB652 - 8406 - 194

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Components

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


Mass: 22048.699 Da / Num. of mol.: 2 / Mutation: I784F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Production host: Escherichia coli (E. coli) / References: UniProt: E9Q401
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsdisease mutation

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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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate (PH4.5), 0.8 M sodium sulphate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 66033 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.069 / Rrim(I) all: 0.173 / Χ2: 0.956 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.483.40.70231280.3940.4180.8240.56595.5
1.48-1.54.10.63232130.6950.3430.7230.5598.6
1.5-1.535.10.61132320.7990.2960.6810.66498.9
1.53-1.565.50.55332730.8510.260.6120.71199.9
1.56-1.65.60.52832760.8710.2450.5840.794100
1.6-1.636.30.68732570.870.2940.7490.85899.9
1.63-1.676.40.67732780.8240.290.7370.92999.9
1.67-1.726.10.60632730.8840.2650.6631.037100
1.72-1.776.40.48933170.9290.2080.5321.053100
1.77-1.836.60.43632920.9350.1820.4731.075100
1.83-1.896.50.36232950.9470.1520.3931.042100
1.89-1.976.40.49232650.880.2120.5361.055100
1.97-2.066.20.19832970.9780.0860.2171.019100
2.06-2.176.50.1833120.9820.0760.1951.055100
2.17-2.36.30.24133230.9220.1080.2651.03599.8
2.3-2.486.60.14533280.9880.0610.1581.015100
2.48-2.736.20.1333250.9880.0570.1421.048100
2.73-3.126.80.11233750.9910.0460.1211100
3.12-3.946.10.10433970.9880.0460.1141.0399.9
3.94-506.10.0835770.9950.0340.0871.02799.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C33

5c33


Resolution: 1.452→29.86 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.2038 2000 3.03 %
Rwork0.1722 --
obs0.1731 65931 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.95 Å2 / Biso mean: 21.5886 Å2 / Biso min: 6.93 Å2
Refinement stepCycle: final / Resolution: 1.452→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 72 508 3473
Biso mean--36.95 31.13 -
Num. residues----379
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1024X-RAY DIFFRACTION14.187TORSIONAL
12B1024X-RAY DIFFRACTION14.187TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4515-1.48780.30721360.23964337447395
1.4878-1.52810.25381390.21714439457898
1.5281-1.5730.22591420.200345574699100
1.573-1.62380.25091400.192344744614100
1.6238-1.68180.23191430.194745514694100
1.6818-1.74920.23191430.196645664709100
1.7492-1.82880.19631420.198945674709100
1.8288-1.92520.2691410.20645284669100
1.9252-2.04570.18741450.166845884733100
2.0457-2.20370.17271420.156845894731100
2.2037-2.42530.18821440.168845664710100
2.4253-2.77610.19581450.163746284773100
2.7761-3.49670.21461460.156846844830100
3.4967-29.86660.17841520.158148575009100

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