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- PDB-6xxf: 1.7 Angstrom crystal structure of Ca/CaM:RyR2 peptide complex -

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Basic information

Entry
Database: PDB / ID: 6xxf
Title1.7 Angstrom crystal structure of Ca/CaM:RyR2 peptide complex
Components
  • Calmodulin-2
  • RyR2 Peptide
KeywordsMETAL BINDING PROTEIN / calcium-binding protein / cardiac muscle contraction / RyR2
Function / homology
Function and homology information


negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / : / adenylate cyclase binding ...negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / : / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / voltage-gated potassium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / positive regulation of protein serine/threonine kinase activity / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / membrane / nucleus / plasma membrane / cytoplasm
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: 1.7 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 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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-2
BBB: RyR2 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5186
Polymers19,3582
Non-polymers1604
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-76 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.916, 41.710, 85.986
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-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
#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.: 140 / 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: 1.85 Å3/Da / Density % sol: 33.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate pH4.5, 0.2M ammonium acetate, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→41.71 Å / Num. obs: 16464 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.061 / Rrim(I) all: 0.111 / Net I/σ(I): 12.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 1201 / CC1/2: 0.87 / Rpim(I) all: 0.375 / Rrim(I) all: 0.664 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCX

2bcx


Resolution: 1.7→37.556 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2052 795 4.843 %
Rwork0.1799 --
all0.181 --
obs-16416 99.903 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.639 Å20 Å20 Å2
2---0.581 Å20 Å2
3----0.058 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 4 140 1456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131324
X-RAY DIFFRACTIONr_bond_other_d0.0360.0181216
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.6531775
X-RAY DIFFRACTIONr_angle_other_deg2.3911.5932831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98724.17779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22415254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.576158
X-RAY DIFFRACTIONr_chiral_restr0.10.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021504
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02264
X-RAY DIFFRACTIONr_nbd_refined0.2350.2371
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.21129
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2677
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0630.2533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.284
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2820.213
X-RAY DIFFRACTIONr_nbd_other0.2410.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.227
X-RAY DIFFRACTIONr_mcbond_it1.981.972658
X-RAY DIFFRACTIONr_mcbond_other1.9781.971657
X-RAY DIFFRACTIONr_mcangle_it2.7072.951819
X-RAY DIFFRACTIONr_mcangle_other2.7082.951820
X-RAY DIFFRACTIONr_scbond_it3.0442.384666
X-RAY DIFFRACTIONr_scbond_other3.0392.383666
X-RAY DIFFRACTIONr_scangle_it4.613.424956
X-RAY DIFFRACTIONr_scangle_other4.6053.423956
X-RAY DIFFRACTIONr_lrange_it5.78325.0851641
X-RAY DIFFRACTIONr_lrange_other5.78125.0781642
LS refinement shell
Resolution (Å)Num. reflection RfreeNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.744451148X-RAY DIFFRACTION99.0864
1.744-1.791581079X-RAY DIFFRACTION100
1.791-1.843631079X-RAY DIFFRACTION100
1.843-1.9571042X-RAY DIFFRACTION100
1.9-1.96257998X-RAY DIFFRACTION100
1.962-2.03150978X-RAY DIFFRACTION100
2.031-2.10751967X-RAY DIFFRACTION100
2.107-2.19342909X-RAY DIFFRACTION99.7901
2.193-2.2945873X-RAY DIFFRACTION99.8912
2.29-2.40146843X-RAY DIFFRACTION100
2.401-2.53144812X-RAY DIFFRACTION99.8833
2.531-2.68438755X-RAY DIFFRACTION100
2.684-2.86829741X-RAY DIFFRACTION100
2.868-3.09721682X-RAY DIFFRACTION100
3.097-3.39144614X-RAY DIFFRACTION100
3.391-3.78821580X-RAY DIFFRACTION100
3.788-4.36829511X-RAY DIFFRACTION100
4.368-5.33526438X-RAY DIFFRACTION100
5.335-7.48319348X-RAY DIFFRACTION100
7.483-37.55610224X-RAY DIFFRACTION100

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