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- PDB-6xy3: 2.0 Angstrom crystal structure of Ca/CaM N53I:RyR2 peptide complex -

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Basic information

Entry
Database: PDB / ID: 6xy3
Title2.0 Angstrom crystal structure of Ca/CaM N53I:RyR2 peptide complex
Components
  • Calmodulin-1
  • RyR2 peptide
KeywordsMETAL BINDING PROTEIN / calcium-binding protein / cardiac muscle contraction / RyR2
Function / homology
Function and homology information


CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / 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 / PKA activation ...CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / 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 / 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 / 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 / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / 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 / RHO GTPases activate PAKs / calcineurin-mediated signaling / 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 / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / 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 / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / centrosome
Similarity search - Function
: / 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 / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAntonyuk, S. / Helassa, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationFS/17/56/32925 United Kingdom
CitationJournal: J.Cell.Sci. / Year: 2022
Title: CPVT-associated calmodulin variants N53I and A102V dysregulate Ca2+ signalling via different mechanisms.
Authors: Prakash, O. / Held, M. / McCormick, L.F. / Gupta, N. / Lian, L.Y. / Antonyuk, S. / Haynes, L.P. / Thomas, N.L. / Helassa, N.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Calmodulin-1
BBB: RyR2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5176
Polymers19,3572
Non-polymers1604
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-73 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.010, 42.700, 89.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin-1


Mass: 16851.600 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 RyR2 peptide


Mass: 2505.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 50 / 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: 1.92 Å3/Da / Density % sol: 36.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.5, 10% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2→89.36 Å / Num. obs: 10637 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.069 / Rrim(I) all: 0.122 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 778 / CC1/2: 0.908 / Rpim(I) all: 0.256 / Rrim(I) all: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XXF

6xxf


Resolution: 2→44.72 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.193
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2597 512 4.834 %
Rwork0.208 --
all0.211 --
obs-10591 99.887 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.154 Å20 Å20 Å2
2--2.248 Å20 Å2
3----2.403 Å2
Refinement stepCycle: LAST / Resolution: 2→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 4 50 1331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131311
X-RAY DIFFRACTIONr_bond_other_d0.0360.0181194
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.6461764
X-RAY DIFFRACTIONr_angle_other_deg2.3941.5932775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1555166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58324.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43615240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.975156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021497
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02257
X-RAY DIFFRACTIONr_nbd_refined0.2260.2365
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.21021
X-RAY DIFFRACTIONr_nbtor_refined0.160.2661
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0570.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.212
X-RAY DIFFRACTIONr_nbd_other0.220.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.214
X-RAY DIFFRACTIONr_mcbond_it2.8783.388667
X-RAY DIFFRACTIONr_mcbond_other2.8713.387666
X-RAY DIFFRACTIONr_mcangle_it4.2725.057832
X-RAY DIFFRACTIONr_mcangle_other4.2715.057833
X-RAY DIFFRACTIONr_scbond_it3.5393.687644
X-RAY DIFFRACTIONr_scbond_other3.5323.686644
X-RAY DIFFRACTIONr_scangle_it5.4385.389932
X-RAY DIFFRACTIONr_scangle_other5.4385.387932
X-RAY DIFFRACTIONr_lrange_it7.41841.1831564
X-RAY DIFFRACTIONr_lrange_other7.41541.1571559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.367350.239734X-RAY DIFFRACTION99.7406
2.052-2.1080.375410.224686X-RAY DIFFRACTION100
2.108-2.1690.25290.207725X-RAY DIFFRACTION99.8676
2.169-2.2360.238330.19666X-RAY DIFFRACTION100
2.236-2.3090.321320.195648X-RAY DIFFRACTION100
2.309-2.390.234300.193626X-RAY DIFFRACTION100
2.39-2.4810.239330.192621X-RAY DIFFRACTION99.5434
2.481-2.5820.239340.211580X-RAY DIFFRACTION100
2.582-2.6960.224270.204568X-RAY DIFFRACTION99.665
2.696-2.8280.281270.221549X-RAY DIFFRACTION100
2.828-2.9810.274300.221516X-RAY DIFFRACTION99.8172
2.981-3.1610.328240.229487X-RAY DIFFRACTION100
3.161-3.3790.323200.234468X-RAY DIFFRACTION100
3.379-3.650.294270.214437X-RAY DIFFRACTION100
3.65-3.9970.232220.208401X-RAY DIFFRACTION100
3.997-4.4680.187180.171385X-RAY DIFFRACTION100
4.468-5.1570.209220.176316X-RAY DIFFRACTION99.705
5.157-6.3110.342110.243293X-RAY DIFFRACTION100
6.311-8.9030.339100.2229X-RAY DIFFRACTION100
8.903-44.720.12370.22144X-RAY DIFFRACTION100

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