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- PDB-7kl5: Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (... -

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Basic information

Entry
Database: PDB / ID: 7kl5
TitleStructure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RyR2) at Residues: Phe4246 to Val4271
Components
  • Calmodulin-1
  • Ryanodine receptor 2
KeywordsMETAL BINDING PROTEIN / Calmodulin / CaM / RyR2 / CaM binding domain / ryanodine receptor
Function / homology
Function and homology information


junctional sarcoplasmic reticulum membrane / sarcoplasmic reticulum calcium ion transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / calcium-induced calcium release activity / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential ...junctional sarcoplasmic reticulum membrane / sarcoplasmic reticulum calcium ion transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / calcium-induced calcium release activity / 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 / cell communication by electrical coupling involved in cardiac conduction / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / 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 / CaM pathway / regulation of cardiac muscle contraction by calcium ion signaling / response to caffeine / Cam-PDE 1 activation / Sodium/Calcium exchangers / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / cellular response to caffeine / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / response to muscle activity / presynaptic endocytosis / protein kinase A regulatory subunit binding / Synthesis of IP3 and IP4 in the cytosol / protein kinase A catalytic subunit binding / regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of the force of heart contraction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / catalytic complex / regulation of cardiac muscle contraction / regulation of cytosolic calcium ion concentration / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of heart rate / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / cardiac muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / response to muscle stretch / release of sequestered calcium ion into cytosol / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / cellular response to epinephrine stimulus / FCERI mediated Ca+2 mobilization / substantia nigra development / sarcoplasmic reticulum membrane / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
Similarity search - Function
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 ...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 / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Ryanodine receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFisher, A.J. / Ames, J.B. / Yu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY012347 United States
CitationJournal: Biochemistry / Year: 2021
Title: The Crystal Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RyR2) at Residues Phe4246-Val4271 Reveals a Fifth Calcium Binding Site.
Authors: Yu, Q. / Anderson, D.E. / Kaur, R. / Fisher, A.J. / Ames, J.B.
History
DepositionOct 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-1
B: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,95411
Polymers20,5052
Non-polymers4499
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-81 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.169, 62.403, 43.190
Angle α, β, γ (deg.)90.000, 107.494, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide Ryanodine receptor 2 / RYR-2 / RyR2 / hRYR-2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor- ...RYR-2 / RyR2 / hRYR-2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor


Mass: 3652.701 Da / Num. of mol.: 1 / Fragment: Phe4246 to Thr4275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92736
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium acetate, 0.1M Tris pH 8.5, 30%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2018
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.65→62.4 Å / Num. obs: 19805 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Net I/σ(I): 9.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3226 / CC1/2: 0.81 / Rrim(I) all: 1.03 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Jan 26, 2018 BUILT=20180319data reduction
Aimless0.7.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bcx

2bcx


Resolution: 1.65→41.192 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.093 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2455 980 4.953 %
Rwork0.2091 18806 -
all0.211 --
obs-19786 97.68 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.159 Å2
Baniso -1Baniso -2Baniso -3
1-2.936 Å20 Å2-0.192 Å2
2--1.294 Å2-0 Å2
3----3.428 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 21 72 1472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131423
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171378
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.6571897
X-RAY DIFFRACTIONr_angle_other_deg1.4611.5933192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9785177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78924.44481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.635158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
X-RAY DIFFRACTIONr_nbd_refined0.2460.2372
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21291
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2693
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.261
X-RAY DIFFRACTIONr_metal_ion_refined0.2030.224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.219
X-RAY DIFFRACTIONr_nbd_other0.2420.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.28
X-RAY DIFFRACTIONr_mcbond_it2.0362.675696
X-RAY DIFFRACTIONr_mcbond_other2.0142.669695
X-RAY DIFFRACTIONr_mcangle_it3.0463.99868
X-RAY DIFFRACTIONr_mcangle_other3.0483.996869
X-RAY DIFFRACTIONr_scbond_it2.6913.052727
X-RAY DIFFRACTIONr_scbond_other2.693.057728
X-RAY DIFFRACTIONr_scangle_it4.134.4051026
X-RAY DIFFRACTIONr_scangle_other4.1284.4111027
X-RAY DIFFRACTIONr_lrange_it6.29832.6981677
X-RAY DIFFRACTIONr_lrange_other6.29532.6981677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.65-1.6930.339720.36613460.36514730.4340.43596.26610.349
1.693-1.7390.291590.3513480.34714470.5770.52897.23570.335
1.739-1.7890.331710.28812830.2914100.6810.66996.02840.27
1.789-1.8440.25670.27113010.2714010.780.79897.64450.258
1.844-1.9050.273550.24712240.24913030.8560.85798.15810.235
1.905-1.9720.304650.22112100.22512920.8560.88998.68420.214
1.972-2.0460.226570.21211860.21212590.8980.90198.72910.213
2.046-2.1290.278500.21711090.2211790.9060.91398.30360.22
2.129-2.2230.206590.21610930.21611690.9210.92198.54580.225
2.223-2.3320.219470.21310070.21310720.9190.92198.32090.231
2.332-2.4570.246540.2129760.21410490.9030.92198.18880.237
2.457-2.6060.333570.2229160.22810030.8870.91797.0090.253
2.606-2.7850.286640.2068480.2119230.9140.93598.80820.244
2.785-3.0070.238370.1958310.1978810.9240.93698.52440.235
3.007-3.2920.238470.2257400.2267970.9230.92898.74530.272
3.292-3.6780.277340.2066860.2097310.9190.93598.49520.259
3.678-4.2410.178270.1766020.1766370.9510.95498.74410.225
4.241-5.1810.157290.1664990.1665480.9670.96896.35040.226
5.181-7.2690.263180.2124030.2144250.9230.94499.05880.282
7.269-41.1920.366110.2051970.2122560.8850.94481.250.25
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)
11.46310.2897-1.18151.0464-0.30933.9539-0.0193-0.17340.0086-0.03870.0642-0.0708-0.02460.0003-0.04490.10170.0114-0.01230.0781-0.00860.0518-16.12914.54320.983
20.7714-0.2473-1.08281.61350.69574.7687-0.2535-0.15090.022-0.08410.1940.15970.57790.42720.05950.21840.04520.01910.0570.02440.0787-20.2064.43441.852
310.3344-4.38043.20912.081-3.11515.1524-0.1056-0.17920.1241-0.0081-0.006-0.05370.23490.98840.11160.1876-0.0561-0.00010.22670.00660.0901-19.4919.99932.213
416.0183-11.54534.47328.7658-2.32034.195-0.3421-0.21710.6290.26290.0386-0.3041-0.4157-0.10490.30350.2662-0.0390.00740.1282-0.00720.2105-33.2321.69224.412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 76
2X-RAY DIFFRACTION2ALLA77 - 147
3X-RAY DIFFRACTION3ALLB1 - 11
4X-RAY DIFFRACTION4ALLB12 - 27

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