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- PDB-5j8h: Structure of calmodulin in a complex with a peptide derived from ... -

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Basic information

Entry
Database: PDB / ID: 5j8h
TitleStructure of calmodulin in a complex with a peptide derived from a calmodulin-dependent kinase
Components
  • Calmodulin
  • Eukaryotic elongation factor 2 kinase
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / Calmodulin eEF2K complex kinase / METAL BINDING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


elongation factor 2 kinase / elongation factor-2 kinase activity / response to prolactin / regulation of translation at postsynapse / myosin II filament disassembly / cellular response to anoxia / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : ...elongation factor 2 kinase / elongation factor-2 kinase activity / response to prolactin / regulation of translation at postsynapse / myosin II filament disassembly / cellular response to anoxia / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / positive regulation of dendritic spine morphogenesis / translation factor activity, RNA binding / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of peptidyl-threonine phosphorylation / positive regulation of synapse assembly / 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 / positive regulation of DNA binding / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / nitric-oxide synthase binding / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / 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 ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / regulation of synaptic vesicle endocytosis / positive regulation of endocytosis / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / positive regulation of protein autophosphorylation / mTORC1-mediated signalling / Long-term potentiation / protein phosphatase activator activity / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / translational elongation / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / 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 / activation of adenylate cyclase activity / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / cellular response to brain-derived neurotrophic factor stimulus / cellular response to cAMP / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / FCERI mediated Ca+2 mobilization / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of nitric-oxide synthase activity / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity
Similarity search - Function
Eukaryotic elongation factor 2 kinase / : / : / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / : / EF-hand domain pair / EF-hand, calcium binding motif ...Eukaryotic elongation factor 2 kinase / : / : / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / : / 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 / Tetratricopeptide-like helical domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Eukaryotic elongation factor 2 kinase / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAlphonse, S. / Lee, K. / Piserchio, A. / Tavares, C.D.J. / Giles, D.H. / Wellmann, R.M. / Dalby, K.N. / Ghose, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084278 United States
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)G12 MD007603 United States
CitationJournal: Structure / Year: 2016
Title: Structural Basis for the Recognition of Eukaryotic Elongation Factor 2 Kinase by Calmodulin.
Authors: Lee, K. / Alphonse, S. / Piserchio, A. / Tavares, C.D. / Giles, D.H. / Wellmann, R.M. / Dalby, K.N. / Ghose, R.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Eukaryotic elongation factor 2 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9694
Polymers19,8892
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3090 Å2
ΔGint-33 kcal/mol
Surface area9240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pET28b / Details (production host): pET28b-His-SUMO-CaM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Eukaryotic elongation factor 2 kinase / eEF-2K / Calcium/calmodulin-dependent eukaryotic elongation factor 2 kinase


Mass: 3167.618 Da / Num. of mol.: 1 / Fragment: residues 74-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF2K / Plasmid: pET28b / Details (production host): pET28b-His-SUMO-CBD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O00418, elongation factor 2 kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic43D HNCO
121isotropic43D HN(CA)CO
131isotropic43D CBCA(CO)NH
141isotropic23D HN(CA)CB
151isotropic53D H(CCO)NH
161isotropic43D C(CO)NH
171isotropic43D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY aliphatic
3103isotropic13D 1H-13C NOESY aromatic
3113isotropic13D 1H-13C NOESY aliphatic 13C-filtered
2122isotropic53D HNCO
2132isotropic13D CBCA(CO)NH
2142isotropic13D HN(CA)CB
2152isotropic33D HNCA
2162isotropic33D H(CCO)NH
2172isotropic43D C(CO)NH
2182isotropic23D (H)CCH-TOCSY
2192isotropic33D 1H-15N NOESY
2202isotropic53D 1H-13C NOESY aromatic
4214isotropic13D 1H-13C NOESY aromatic
4224isotropic13D 1H-13C NOESY aliphatic 13C filtered

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1320 uM [U-99% 13C; U-99% 15N] Calmodulin, 320 uM eEF2K_74-100, 95% H2O/5% D2OCaMPep_w95% H2O/5% D2O
solution2595 uM [U-99% 13C; U-99% 15N] eEF2K_74-100, 595 uM Calmodulin, 95% H2O/5% D2OPepCaM_w95% H2O/5% D2O
solution3320 uM [U-99% 13C; U-99% 15N] Calmodulin, 320 uM eEF2K_74-100, 100% D2OCaMPep_d100% D2O
solution4320 uM [U-99% 13C; U-99% 15N] eEF2K_74-100, 320 uM Calmodulin, 100% D2OPepCaM_d100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
320 uMCalmodulin[U-99% 13C; U-99% 15N]1
320 uMeEF2K_74-100natural abundance1
595 uMeEF2K_74-100[U-99% 13C; U-99% 15N]2
595 uMCalmodulinnatural abundance2
320 uMCalmodulin[U-99% 13C; U-99% 15N]3
320 uMeEF2K_74-100natural abundance3
320 uMeEF2K_74-100[U-99% 13C; U-99% 15N]4
320 uMCalmodulinnatural abundance4
Sample conditions

Ionic strength: 20 mM BisTris 150 mM Potassium Chloride 10 mM Calcium Chloride mM / Pressure: 1 atm / Temperature: 308.15 K

Conditions-IDLabelpHPH errTemperature err
1H2O6.80.20.1
2H2O6.80.2
3D2O6.8 pD
4D2O6.8 pD

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE9003
Bruker AVANCEBrukerAVANCE5005
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure calculation
Xplor_NIH2.4NIH C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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