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- PDB-6xxx: 1.25 Angstrom crystal structure of Ca/CaM A102V:RyR2 peptide complex -

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Basic information

Entry
Database: PDB / ID: 6xxx
Title1.25 Angstrom crystal structure of Ca/CaM A102V:RyR2 peptide complex
Components
  • Calmodulin-1
  • LYS-LYS-ALA-VAL-TRP-HIS-LYS-LEU-LEU-SER-LYS-GLN-ARG-LYS-ARG-ALA-VAL-VAL-ALA-CYS-PHE
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: 1.25 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 28, 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

Downloads & links

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Assembly

Deposited unit
AAA: Calmodulin-1
BBB: LYS-LYS-ALA-VAL-TRP-HIS-LYS-LEU-LEU-SER-LYS-GLN-ARG-LYS-ARG-ALA-VAL-VAL-ALA-CYS-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5466
Polymers19,3862
Non-polymers1604
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-74 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.110, 41.800, 86.020
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: 16880.600 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 LYS-LYS-ALA-VAL-TRP-HIS-LYS-LEU-LEU-SER-LYS-GLN-ARG-LYS-ARG-ALA-VAL-VAL-ALA-CYS-PHE


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.: 209 / 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: 1.87 Å3/Da / Density % sol: 34.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.0, 25% w/v Polyethylene glycol 1,500

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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: 1.23→41.8 Å / Num. obs: 42088 / % possible obs: 98.37 % / Redundancy: 5.6 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.017 / Rrim(I) all: 0.042 / Net I/σ(I): 18.4
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1739 / CC1/2: 0.473 / Rpim(I) all: 0.553 / Rrim(I) all: 0.971 / % possible all: 83.25

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XXF

6xxf


Resolution: 1.25→37.624 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.152 / SU B: 3.229 / SU ML: 0.057 / Average fsc free: 0.9421 / Average fsc work: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1892 2015 4.988 %
Rwork0.1417 38384 -
all0.144 --
obs-40399 98.952 %
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: 23.636 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2--3.864 Å20 Å2
3----2.594 Å2
Refinement stepCycle: LAST / Resolution: 1.25→37.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 4 209 1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131426
X-RAY DIFFRACTIONr_bond_other_d0.0060.0181319
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.6571927
X-RAY DIFFRACTIONr_angle_other_deg1.6811.5933085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71823.69692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63915285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1971511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021648
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02293
X-RAY DIFFRACTIONr_nbd_refined0.2420.2418
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21219
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2709
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2070.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.221
X-RAY DIFFRACTIONr_nbd_other0.2440.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.240
X-RAY DIFFRACTIONr_mcbond_it3.3392.118691
X-RAY DIFFRACTIONr_mcbond_other3.3372.117690
X-RAY DIFFRACTIONr_mcangle_it3.673.184867
X-RAY DIFFRACTIONr_mcangle_other3.6693.185868
X-RAY DIFFRACTIONr_scbond_it5.4792.586735
X-RAY DIFFRACTIONr_scbond_other5.4792.585735
X-RAY DIFFRACTIONr_scangle_it6.1943.7221050
X-RAY DIFFRACTIONr_scangle_other6.1943.7211050
X-RAY DIFFRACTIONr_lrange_it6.0927.761829
X-RAY DIFFRACTIONr_lrange_other5.76727.1381783
X-RAY DIFFRACTIONr_rigid_bond_restr13.18732745
LS refinement shellResolution: 1.25→1.282 Å
RfactorNum. reflection% reflection
Rfree0.286 113 -
Rwork0.275 2572 -
obs--90.9553 %

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