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- PDB-7zrq: 1.68 Angstrom crystal structure of Ca/CaM-E140G:CaMKIIdelta pepti... -

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Basic information

Entry
Database: PDB / ID: 7zrq
Title1.68 Angstrom crystal structure of Ca/CaM-E140G:CaMKIIdelta peptide complex
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit delta
  • Calmodulin-1
KeywordsMETAL BINDING PROTEIN / calcium-binding protein / calmodulin / CaM / CaMKII / kinase
Function / homology
Function and homology information


regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors / cardiac muscle cell contraction / endoplasmic reticulum calcium ion homeostasis / Assembly and cell surface presentation of NMDA receptors / sodium channel inhibitor activity / calmodulin-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of heart contraction / Calmodulin induced events / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / relaxation of cardiac muscle / 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 / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / regulation of membrane depolarization / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / HSF1-dependent transactivation / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / sarcoplasmic reticulum membrane / calcium channel complex / substantia nigra development / cellular response to calcium ion / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of cell growth
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Calmodulin-1 / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsHelassa, N. / Antonyuk, S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
British Heart FoundationFS/17/56/32925 United Kingdom
Wellcome Trust102172/B/13/Z United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Calmodulin variant E140G associated with long QT syndrome impairs CaMKII delta autophosphorylation and L-type calcium channel inactivation.
Authors: Prakash, O. / Gupta, N. / Milburn, A. / McCormick, L. / Deugi, V. / Fisch, P. / Wyles, J. / Thomas, N.L. / Antonyuk, S. / Dart, C. / Helassa, N.
History
DepositionMay 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
B: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4177
Polymers19,1642
Non-polymers2525
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-72 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.380, 54.520, 57.500
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: 16649.287 Da / Num. of mol.: 1 / Mutation: E140G
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 Calcium/calmodulin-dependent protein kinase type II subunit delta / CaM kinase II subunit delta / CaMK-II subunit delta


Mass: 2515.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Source: (synth.) Homo sapiens (human) / Feature type: SUBJECT OF INVESTIGATION / References: Ca2+/calmodulin-dependent protein kinase
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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 % sol: 27.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na+-HEPES, 0.1 M MOPS (acid), pH 7.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.68→39.59 Å / Num. obs: 15287 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Net I/σ(I): 13.5
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 2.042 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 684 / CC1/2: 0.311 / Rpim(I) all: 1.452 / Rrim(I) all: 2.522 / % possible all: 87.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0350refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WEL

2wel


Resolution: 1.68→39.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 9.797 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2439 802 5.261 %
Rwork0.2052 14442 -
all0.207 --
obs-15244 99.084 %
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: 29.842 Å2
Baniso -1Baniso -2Baniso -3
1--3.559 Å20 Å2-0 Å2
2--0.736 Å20 Å2
3---2.823 Å2
Refinement stepCycle: LAST / Resolution: 1.68→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 10 39 1337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121343
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161201
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.6481772
X-RAY DIFFRACTIONr_angle_other_deg0.4671.5622811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.283109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86610252
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3881071
X-RAY DIFFRACTIONr_chiral_restr0.0660.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02245
X-RAY DIFFRACTIONr_nbd_refined0.2510.2322
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21110
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2674
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.247
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3580.220
X-RAY DIFFRACTIONr_nbd_other0.2230.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.540.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.120.21
X-RAY DIFFRACTIONr_mcbond_it2.2082.872665
X-RAY DIFFRACTIONr_mcbond_other2.1592.873665
X-RAY DIFFRACTIONr_mcangle_it3.1574.294825
X-RAY DIFFRACTIONr_mcangle_other3.1554.298826
X-RAY DIFFRACTIONr_scbond_it3.0763.249678
X-RAY DIFFRACTIONr_scbond_other3.0743.254679
X-RAY DIFFRACTIONr_scangle_it4.6674.76946
X-RAY DIFFRACTIONr_scangle_other4.6644.765947
X-RAY DIFFRACTIONr_lrange_it6.75248.7691554
X-RAY DIFFRACTIONr_lrange_other6.73648.7861554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.7240.36600.43930X-RAY DIFFRACTION88.551
1.724-1.7710.357580.3761011X-RAY DIFFRACTION99.0732
1.771-1.8220.359570.3421010X-RAY DIFFRACTION99.9064
1.822-1.8780.267490.302981X-RAY DIFFRACTION100
1.878-1.940.342430.275955X-RAY DIFFRACTION99.8999
1.94-2.0070.277600.244884X-RAY DIFFRACTION99.8942
2.007-2.0830.223510.232909X-RAY DIFFRACTION100
2.083-2.1680.354370.231850X-RAY DIFFRACTION100
2.168-2.2640.277330.215830X-RAY DIFFRACTION100
2.264-2.3740.257460.199789X-RAY DIFFRACTION100
2.374-2.5020.224380.192752X-RAY DIFFRACTION100
2.502-2.6530.339530.181703X-RAY DIFFRACTION100
2.653-2.8350.29340.197677X-RAY DIFFRACTION100
2.835-3.0610.222320.204634X-RAY DIFFRACTION100
3.061-3.3510.255350.19575X-RAY DIFFRACTION100
3.351-3.7440.175360.174532X-RAY DIFFRACTION100
3.744-4.3160.225220.159475X-RAY DIFFRACTION100
4.316-5.2710.238280.162413X-RAY DIFFRACTION100
5.271-7.3890.345110.238331X-RAY DIFFRACTION100
7.389-39.590.175190.213201X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.66291.48730.96981.19710.6121.0242-0.05330.07630.2738-0.19020.0395-0.0305-0.03580.03570.01390.1770.0340.02050.05870.00220.056417.1754-0.03961.8951
23.6941-3.50540.57587.5505-0.56032.50290.03880.05530.1483-0.1108-0.0153-0.0355-0.05360.0074-0.02340.0553-0.0252-0.00380.0618-0.01260.018720.6308-2.08691.329
Refinement TLS groupSelection: ALL

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