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- PDB-6y4o: Calmodulin bound to cardiac ryanodine receptor (RyR2) calmodulin ... -

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Basic information

Entry
Database: PDB / ID: 6y4o
TitleCalmodulin bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain
Components
  • Calmodulin-2
  • Ryanodine receptor 2
KeywordsMEMBRANE PROTEIN / ion channel / calcium / calmodulin
Function / homology
Function and homology information


manganese ion transmembrane transport / negative regulation of calcium ion transmembrane transporter activity / junctional sarcoplasmic reticulum membrane / 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 ...manganese ion transmembrane transport / negative regulation of calcium ion transmembrane transporter activity / junctional sarcoplasmic reticulum membrane / 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 / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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 / regulation of cardiac muscle contraction by calcium ion signaling / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / CaM pathway / Cam-PDE 1 activation / calcium ion transport into cytosol / Sodium/Calcium exchangers / calcium ion transmembrane import into cytosol / response to caffeine / A band / cell communication by electrical coupling involved in cardiac conduction / Calmodulin induced events / response to redox state / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / positive regulation of cyclic-nucleotide phosphodiesterase activity / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of heart rate / Activation of RAC1 downstream of NMDARs / negative regulation of cytosolic calcium ion concentration / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / cellular response to caffeine / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein kinase A regulatory subunit binding / protein phosphatase activator activity / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / RHO GTPases activate PAKs / positive regulation of the force of heart contraction / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / response to magnesium ion / Long-term potentiation / Uptake and function of anthrax toxins / : / adenylate cyclase binding / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / smooth endoplasmic reticulum / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / calcium channel inhibitor activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / eNOS activation / Activation of AMPK downstream of NMDARs / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / release of sequestered calcium ion into cytosol / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Ion homeostasis
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. / 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
Similarity search - Domain/homology
Ryanodine receptor 2 / Calmodulin-1 / Calmodulin-2 / Ryanodine receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83549081766 Å
AuthorsLau, K. / Nielsen, L.H. / Holt, C. / Brohus, M. / Sorensen, A.B. / Larsen, K.T. / Sommer, C. / Van Petegem, F. / Overgaard, M.T. / Wimmer, R.
Funding support Denmark, Germany, Canada, 4items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-1323-00344 Denmark
Novo Nordisk FoundationNNF18OC0053032 Denmark
European Union (EU)261863 Germany
Canadian Institutes of Health Research (CIHR)PJT-148632 Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The arrhythmogenic N53I variant subtly changes the structure and dynamics in the calmodulin N-terminal domain, altering its interaction with the cardiac ryanodine receptor.
Authors: Holt, C. / Hamborg, L. / Lau, K. / Brohus, M. / Sorensen, A.B. / Larsen, K.T. / Sommer, C. / Van Petegem, F. / Overgaard, M.T. / Wimmer, R.
History
DepositionFeb 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Jan 24, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,4916
Polymers20,3312
Non-polymers1604
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Confirmed by NMR
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-79 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.037, 43.557, 90.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Calmodulin-2


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2, CAM2, CAMB / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP24, UniProt: P0DP23*PLUS
#2: Protein/peptide 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: 3478.235 Da / Num. of mol.: 1
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, UniProt: Q92736*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.84 Å3/Da / Density % sol: 32.99 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Acetate pH 4.70 and 23 % PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83549081766→27.3032443034 Å / Num. obs: 13605 / % possible obs: 99.17 % / Redundancy: 6.2 % / Biso Wilson estimate: 29.9787078079 Å2 / CC1/2: 1 / Net I/σ(I): 21.7
Reflection shellResolution: 1.84→1.87 Å / Num. unique obs: 765 / CC1/2: 0.854

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bcx

2bcx


Resolution: 1.83549081766→27.3032443034 Å / SU ML: 0.143956941533 / Cross valid method: FREE R-VALUE / σ(F): 1.3667843413 / Phase error: 20.1773454449
RfactorNum. reflection% reflection
Rfree0.207570641712 1357 10.0095891421 %
Rwork0.176528109574 --
obs0.179726606149 13557 99.2169203747 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.9404278629 Å2
Refinement stepCycle: LAST / Resolution: 1.83549081766→27.3032443034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 4 49 1255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009189562656931220
X-RAY DIFFRACTIONf_angle_d0.9049032374571646
X-RAY DIFFRACTIONf_chiral_restr0.0489137515139190
X-RAY DIFFRACTIONf_plane_restr0.00588164999826217
X-RAY DIFFRACTIONf_dihedral_angle_d11.424215562735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8355-1.90110.2283396177051270.2254546107211146X-RAY DIFFRACTION94.6468401487
1.9011-1.97720.2684809552711340.1980983404881198X-RAY DIFFRACTION99.9249812453
1.9772-2.06710.2560362713391340.1752603958571208X-RAY DIFFRACTION99.9255398362
2.0671-2.17610.2047526971011340.1603548560711204X-RAY DIFFRACTION99.7019374069
2.1761-2.31230.226024827081340.1646973024881211X-RAY DIFFRACTION100
2.3123-2.49080.2024329581391350.1628094447321207X-RAY DIFFRACTION99.9255398362
2.4908-2.74120.2142027946391370.1752661151381240X-RAY DIFFRACTION99.9274310595
2.7412-3.13740.2158433685891370.1893233012721232X-RAY DIFFRACTION99.9270072993
3.1374-3.95080.178315744021380.1729431528541244X-RAY DIFFRACTION99.2816091954
3.9508-27.30324430340.2071423776041470.1767727913521310X-RAY DIFFRACTION98.9137813985

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