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- PDB-6y4p: Calmodulin N53I variant bound to cardiac ryanodine receptor (RyR2... -

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Basic information

Entry
Database: PDB / ID: 6y4p
TitleCalmodulin N53I variant bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain
Components
  • Calmodulin-1
  • Ryanodine receptor 2
KeywordsMEMBRANE PROTEIN / ion channel / calcium / calmodulin
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 / : / Stimuli-sensing channels / cell communication by electrical coupling involved in cardiac conduction / 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 / CaM pathway / ryanodine-sensitive calcium-release channel activity / Cam-PDE 1 activation / Sodium/Calcium exchangers / response to caffeine / regulation of cardiac muscle contraction by calcium ion signaling / Calmodulin induced events / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Reduction of cytosolic Ca++ levels / response to redox state / 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 / calcium ion transmembrane import into cytosol / PKA activation / CaMK IV-mediated phosphorylation of CREB / 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 calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / response to muscle activity / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / protein kinase A regulatory subunit binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / protein kinase A catalytic subunit binding / cellular response to caffeine / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of the force of heart contraction / RHO GTPases activate PAKs / calcineurin-mediated signaling / intracellularly gated calcium channel activity / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / 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 / smooth endoplasmic reticulum / presynaptic cytosol / calcium channel inhibitor activity / positive regulation of heart rate / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / response to muscle stretch / sarcoplasmic reticulum membrane / release of sequestered calcium ion into cytosol / cellular response to epinephrine stimulus / sperm midpiece / substantia nigra development / calcium channel complex
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
Ryanodine receptor 2 / Calmodulin-1 / Ryanodine receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13325578805 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-1
B: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4906
Polymers20,3302
Non-polymers1604
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-78 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.590, 42.360, 90.360
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-1


Mass: 16851.600 Da / Num. of mol.: 1 / Mutation: N53I
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 / 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.: 61 / 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

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: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.133→45.18 Å / Num. obs: 8489 / % possible obs: 99.76 % / Redundancy: 5.9 % / Biso Wilson estimate: 24.3986621334 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.45
Reflection shellResolution: 2.133→2.209 Å / Num. unique obs: 831 / CC1/2: 0.946

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Processing

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

2bcx


Resolution: 2.13325578805→45.1799 Å / SU ML: 0.232891903909 / Cross valid method: FREE R-VALUE / σ(F): 1.43770529883 / Phase error: 21.642731085
RfactorNum. reflection% reflection
Rfree0.246214623017 848 9.98939804453 %
Rwork0.182375524054 --
obs0.188711047719 8489 99.7649547538 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.4527987444 Å2
Refinement stepCycle: LAST / Resolution: 2.13325578805→45.1799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 4 61 1306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763994865661259
X-RAY DIFFRACTIONf_angle_d0.7354846491261696
X-RAY DIFFRACTIONf_chiral_restr0.0413301689464195
X-RAY DIFFRACTIONf_plane_restr0.00517412175929223
X-RAY DIFFRACTIONf_dihedral_angle_d2.41324828376816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1333-2.26690.2520705967541390.1805671908061260X-RAY DIFFRACTION99.71489665
2.2669-2.44190.2811408234221370.1793005509691228X-RAY DIFFRACTION99.707815924
2.4419-2.68760.259734827461400.1874431334851255X-RAY DIFFRACTION99.6428571429
2.6876-3.07650.2131511644771400.1993049204531255X-RAY DIFFRACTION100
3.0765-3.87570.2743301015121420.1788047634651281X-RAY DIFFRACTION99.8596491228
3.8757-45.17990.226325429981500.1773019574971362X-RAY DIFFRACTION99.7361477573

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