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- PDB-7zrp: 2.65 Angstrom crystal structure of Ca/CaM:CaMKIIdelta peptide complex -

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Basic information

Entry
Database: PDB / ID: 7zrp
Title2.65 Angstrom crystal structure of Ca/CaM: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 / regulation of cardiac muscle cell action potential involved in regulation of contraction / calcium- and calmodulin-dependent protein kinase complex / regulation of cell communication by electrical coupling / : / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / calcium- and calmodulin-dependent protein kinase complex / regulation of cell communication by electrical coupling / : / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction / Trafficking of AMPA receptors / endoplasmic reticulum calcium ion homeostasis / cardiac muscle cell contraction / sodium channel inhibitor activity / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / 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 / relaxation of cardiac muscle / 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 heart contraction / 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 / positive regulation of cardiac muscle hypertrophy / 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 / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of neuronal synaptic plasticity / 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 / HSF1-dependent transactivation / 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 / regulation of protein localization to plasma membrane / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / positive regulation of cardiac muscle cell apoptotic process / 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 / sarcoplasmic reticulum membrane / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / peptidyl-threonine phosphorylation / 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 / cellular response to calcium ion / 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
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 / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / 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: 2.65 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,90925
Polymers38,4734
Non-polymers1,43621
Water64936
1
A: Calmodulin-1
B: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,18114
Polymers19,2362
Non-polymers94512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Calmodulin-1
D: Calcium/calmodulin-dependent protein kinase type II subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,72711
Polymers19,2362
Non-polymers4919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.283, 72.590, 78.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A3 - 145
211A3 - 145
322A1 - 22
422A2 - 23

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein Calmodulin-1


Mass: 16721.350 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase

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Non-polymers , 5 types, 57 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 200 mM Zinc acetate, 100 mM Imidazole pH8.0, 18% PEG3000

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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: 2.65→53.25 Å / Num. obs: 11133 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.102 / Rrim(I) all: 0.185 / Net I/σ(I): 5.9
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.921 / Num. unique obs: 1442 / CC1/2: 0.576 / Rpim(I) all: 1.249 / Rrim(I) all: 2.3

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Processing

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

2wel


Resolution: 2.65→53.244 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.205 / SU B: 18.34 / SU ML: 0.356 / Average fsc free: 0.9334 / Average fsc work: 0.9573 / Cross valid method: THROUGHOUT / ESU R Free: 0.373
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 555 5.004 %RANDOM
Rwork0.2071 10537 --
all0.21 ---
obs-11092 99.964 %-
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: 66.088 Å2
Baniso -1Baniso -2Baniso -3
1--1.179 Å20 Å20 Å2
2--2.633 Å2-0 Å2
3----1.454 Å2
Refinement stepCycle: LAST / Resolution: 2.65→53.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 47 36 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122760
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162424
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.6483595
X-RAY DIFFRACTIONr_angle_other_deg0.4611.5625673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.7841018
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50310507
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.51310147
X-RAY DIFFRACTIONr_chiral_restr0.0590.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
X-RAY DIFFRACTIONr_nbd_refined0.2230.2677
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22308
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21342
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.256
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.216
X-RAY DIFFRACTIONr_nbd_other0.1760.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.25
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0370.21
X-RAY DIFFRACTIONr_mcbond_it5.1916.5421336
X-RAY DIFFRACTIONr_mcbond_other5.1866.5411336
X-RAY DIFFRACTIONr_mcangle_it7.6749.7861653
X-RAY DIFFRACTIONr_mcangle_other7.6739.7861654
X-RAY DIFFRACTIONr_scbond_it6.1377.1781424
X-RAY DIFFRACTIONr_scbond_other6.1357.1771425
X-RAY DIFFRACTIONr_scangle_it9.10710.5291942
X-RAY DIFFRACTIONr_scangle_other9.10410.5281943
X-RAY DIFFRACTIONr_lrange_it11.56491.0173078
X-RAY DIFFRACTIONr_lrange_other11.52890.63074
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.054453
X-RAY DIFFRACTIONr_ncsr_local_group_20.1290.05592
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.098160.05008
12AX-RAY DIFFRACTIONLocal ncs0.098160.05008
23AX-RAY DIFFRACTIONLocal ncs0.129190.05006
24AX-RAY DIFFRACTIONLocal ncs0.129190.05006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.65-2.7190.371450.3097420.3137880.8820.91699.87310.312
2.719-2.7930.282460.3057630.3048090.930.9241000.307
2.793-2.8740.293510.2936890.2937400.9330.9341000.291
2.874-2.9620.385390.2796970.2857370.8910.94299.86430.274
2.962-3.0590.306430.2876870.2887300.9380.9411000.285
3.059-3.1660.334320.2746580.2786900.9220.9451000.264
3.166-3.2850.345370.2546340.2596710.9180.9571000.241
3.285-3.4180.335390.2236050.236440.9440.9681000.211
3.418-3.570.349250.2166080.226330.9360.9711000.199
3.57-3.7430.319240.2325730.2355970.9430.9681000.219
3.743-3.9440.29210.2015470.2055680.9490.9731000.196
3.944-4.1820.21250.1525200.1555450.9650.9841000.151
4.182-4.4690.231180.1394920.1425110.9610.98699.80430.14
4.469-4.8240.247200.1544660.1584870.9570.98699.79470.166
4.824-5.280.201190.1794240.184430.9720.9821000.185
5.28-5.8970.243180.1863920.1884100.9550.9771000.191
5.897-6.7950.39150.1953420.2023570.9170.9741000.206
6.795-8.2880.148140.1483060.1483200.9880.9851000.175
8.288-11.5820.127130.1682410.1662540.9890.9791000.202
11.582-53.2440.345110.3051510.3081620.9020.9231000.37

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