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Basic information

Entry
Database: PDB / ID: 8fo6
TitleNucleotide-free structure of a functional construct of eukaryotic elongation factor 2 kinase.
Components
  • Calmodulin-1
  • Eukaryotic elongation factor 2 kinase
KeywordsTRANSLATION/Transferase / elongation factor 2 kinase / eEF2 / eEF2K / eEF-2K / Calmodulin / TRANSLATION / allostery / TRANSLATION-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 / translation factor activity, RNA binding / positive regulation of dendritic spine morphogenesis / CaM pathway / positive regulation of synapse assembly ...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 / translation factor activity, RNA binding / positive regulation of dendritic spine morphogenesis / CaM pathway / positive regulation of synapse assembly / 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 / CaMK IV-mediated phosphorylation of CREB / PKA activation / 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 ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / mTORC1-mediated signalling / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of endocytosis / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / translational elongation / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / 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 / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / cellular response to brain-derived neurotrophic factor stimulus / cellular response to cAMP / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / cellular response to calcium ion / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / regulation of cytokinesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / response to ischemia / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / Stimuli-sensing channels / RAF activation / Transcriptional activation of mitochondrial biogenesis / RAS processing / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / cellular response to insulin stimulus / spindle pole / Signaling by RAF1 mutants
Similarity search - Function
Eukaryotic elongation factor 2 kinase / : / : / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / Tetratricopeptide repeat domain / : / EF-hand domain pair ...Eukaryotic elongation factor 2 kinase / : / : / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / Tetratricopeptide repeat domain / : / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / EF-hand domain / EF-hand domain pair / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Protein kinase-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic elongation factor 2 kinase / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 Å
AuthorsPiserchio, A. / Isiorho, E.A. / Dalby, K.N. / Ghose, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123252 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: ADP enhances the allosteric activation of eukaryotic elongation factor 2 kinase by calmodulin.
Authors: Piserchio, A. / Long, K.J. / Browning, L.S. / Bohanon, A.L. / Isiorho, E.A. / Dalby, K.N. / Ghose, R.
History
DepositionDec 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic elongation factor 2 kinase
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2485
Polymers77,1022
Non-polymers1463
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-43 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.527, 58.901, 88.394
Angle α, β, γ (deg.)90.000, 109.670, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Eukaryotic elongation factor 2 kinase / eEF-2 kinase / eEF-2K / Calcium/calmodulin-dependent eukaryotic elongation factor 2 kinase


Mass: 60380.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: EEF2K / Gene: EEF2K / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00418, elongation factor 2 kinase
#2: Protein Calmodulin-1


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 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.9
Details: 100 mM Bis-trispropane, 200 mM NaF, 17.6% PEG-3350 (2protein 1solution)
Temp details: Room temperature, uncontrolled

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2022
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.553→73.001 Å / Num. obs: 24680 / % possible obs: 99.9 % / Redundancy: 6.09 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.996 / CC1/2 anomalous: 0.011 / Rmerge(I) obs: 0.1117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.1227 / AbsDiff over sigma anomalous: 0.775 / Net I/σ(I): 10.33 / Num. measured all: 150222 / % possible anomalous: 99.3 / Redundancy anomalous: 3.15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
6.927-73.00160.047524.1477977797130013000.9970.1120.02120.05220.71199.33.2699.7
5.499-6.9276.280.069919.4979397939126512650.996-0.0220.03030.07640.74199.73.2999.8
4.804-5.4995.60.072417.6569106910123412340.9950.0260.03360.080.7999.62.9299.6
4.365-4.8045.820.074518.4672037203123812380.9950.0250.03380.0820.75799.43.0399.9
4.052-4.3655.230.076616.6264356435123012300.9930.0240.03680.08530.76698.92.7299.4
3.813-4.0525.670.091415.3170827082124912490.9940.0050.04250.1010.75698.72.9499.8
3.622-3.8135.890.105513.8372727272123512350.991-0.1450.04840.11640.80999.43.0499.9
3.464-3.6226.020.117912.6373687368122412240.991-0.0170.05320.12970.79999.23.1199.8
3.331-3.4646.10.135911.3675147514123112310.988-0.1830.06140.14960.79498.73.1699.9
3.216-3.3316.210.16869.4375817581122012200.986-0.0720.0750.1850.81599.53.2100
3.116-3.2166.310.19328.477447744122712270.987-0.080.08460.21130.78499.53.2499.9
3.026-3.1166.340.2277.2579167916124812480.982-0.0530.09890.24810.78199.73.25100
2.947-3.0266.410.26996.3375877587118411840.977-0.0270.11670.29450.76399.93.2899.9
2.875-2.9476.440.34735.1180238023124612460.9630.0170.14950.37880.81299.33.31100
2.81-2.8756.520.42044.3979827982122512250.947-0.0410.17880.45750.7841003.33100
2.75-2.816.440.46873.9380348034124812480.9450.0290.20180.51120.78299.83.2999.9
2.695-2.756.520.5523.478567856120412040.921-0.0050.23450.60070.76699.73.34100
2.644-2.6956.270.65252.7676837683122612260.916-0.010.28260.71240.77699.53.21100
2.597-2.6445.820.80422.2670877087121812180.821-0.0180.36120.88350.75898.5399.9
2.553-2.5975.870.79642.3172097209122812280.838-0.0340.35660.87460.7698.43.04100

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20210224data processing
Aimless0.7.7data scaling
TRUNCATE7.1.018data processing
PHENIX1.20.1_4487refinement
XDSJan 10, 2022data reduction
PHASER1.20.1_4487phasing
ISOLDE1.4refinement
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SHQ

7shq


Resolution: 2.553→47.52 Å / SU ML: 0.3048 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 1153 4.68 %
Rwork0.2169 23497 -
obs0.2176 24650 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.06 Å2
Refinement stepCycle: LAST / Resolution: 2.553→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 3 107 4849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294833
X-RAY DIFFRACTIONf_angle_d0.56086517
X-RAY DIFFRACTIONf_chiral_restr0.0379681
X-RAY DIFFRACTIONf_plane_restr0.0042867
X-RAY DIFFRACTIONf_dihedral_angle_d16.72281754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.553-2.670.3481450.34592917X-RAY DIFFRACTION99.77
2.67-2.810.25421480.27652906X-RAY DIFFRACTION99.9
2.81-2.990.29331280.25892924X-RAY DIFFRACTION99.97
2.99-3.220.28141360.26112938X-RAY DIFFRACTION99.84
3.22-3.540.24171550.21982930X-RAY DIFFRACTION99.9
3.54-4.050.22971440.19742928X-RAY DIFFRACTION99.81
4.05-5.10.18061310.17342961X-RAY DIFFRACTION99.71
5.1-47.520.20951660.20132993X-RAY DIFFRACTION99.25

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