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Basic information

Entry
Database: PDB / ID: 8fny
TitleNucleotide-bound 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 / ATP / ADP / 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 / positive regulation of dendritic spine morphogenesis / translation factor activity, RNA binding / positive regulation of synapse assembly / CaM pathway ...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 dendritic spine morphogenesis / translation factor activity, RNA binding / 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 / 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 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 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 / positive regulation of endocytosis / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / mTORC1-mediated signalling / 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 / translational elongation / Smooth Muscle Contraction / catalytic complex / 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 / 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 / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / 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 / 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 / response to ischemia / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / cellular response to insulin stimulus / response to calcium ion / RAS processing / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Eukaryotic elongation factor 2 kinase / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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
C: Eukaryotic elongation factor 2 kinase
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,36414
Polymers154,2044
Non-polymers2,16010
Water5,567309
1
A: Eukaryotic elongation factor 2 kinase
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1827
Polymers77,1022
Non-polymers1,0805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Eukaryotic elongation factor 2 kinase
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1827
Polymers77,1022
Non-polymers1,0805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.160, 83.352, 88.978
Angle α, β, γ (deg.)65.350, 90.030, 86.470
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 79 through 135 or resid 137...
d_2ens_1(chain "C" and (resid 79 through 90 or (resid 91...
d_1ens_2(chain "B" and (resid 81 or (resid 82 and (name...
d_2ens_2(chain "D" and (resid 81 through 118 or (resid 119...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PHESERA3 - 59
d_12ens_1PROGLYA61 - 158
d_13ens_1TYRASPA160 - 172
d_14ens_1ASNLYSA174 - 265
d_15ens_1ALAGLUA270 - 327
d_16ens_1GLUMETA330 - 432
d_17ens_1GLUGLUA434 - 496
d_18ens_1ATPATPB
d_19ens_1ADPADPC
d_21ens_1PHESERE1 - 57
d_22ens_1PROGLYE59 - 156
d_23ens_1TYRLYSE158 - 296
d_24ens_1ILEMETE298 - 424
d_25ens_1GLUGLUE427 - 489
d_26ens_1ATPATPF
d_27ens_1ADPADPG
d_11ens_2SERALAD4 - 70
d_21ens_2SERALAH1 - 67

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999866608845, 0.0141393268763, -0.00817581507593), (0.014123448858, -0.999898265795, -0.00199656036154), (-0.00820321333547, 0.00188082333196, -0.99996458427)29.1814835178, 36.6774703717, -40.0021541429
2given(0.999877883629, 0.0141564790606, -0.00661905806613), (0.0141638212026, -0.999899122285, 0.00106368319351), (-0.00660333234182, -0.00115730445535, -0.999977528072)29.3551022086, 36.754904158, -40.0714976428

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Components

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Protein , 2 types, 4 molecules ACBD

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 2
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 BL21(DE3) (bacteria) / References: UniProt: P0DP23

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Non-polymers , 5 types, 319 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM Bis-trispropane, 100 mM NaF, 20.5 % w/v PEG-3350 (2protein/1solution)
Temp details: roon 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-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2022 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.22→80.836 Å / Num. obs: 38423 / % possible obs: 89.1 % / Redundancy: 3.64 % / CC1/2: 0.98 / Rmerge(I) obs: 0.1744 / Rpim(I) all: 0.1068 / Rrim(I) all: 0.2051 / Net I/σ(I): 3.55
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 anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
7.535-80.8363.780.08247.1472627262192019200.990.0130.04930.09620.44798.398.898.398.898.31.998.8
5.986-7.5353.890.11855.6974847484192219220.983-0.1030.06990.13760.50599.399.599.399.599.31.9599.5
5.231-5.9863.880.14344.9174557455192019200.977-0.0830.08410.16640.52298.899.298.899.298.81.9599.2
4.758-5.2313.330.12154.964096409192219220.979-0.0660.07850.14540.52996999699961.6999
4.414-4.7583.580.12635.0968866886192119210.977-0.0680.07820.1490.52196.79996.79996.71.8199
4.152-4.4143.660.13274.9470427042192219220.979-0.0920.08070.15560.54495.998.995.998.995.91.8698.9
3.943-4.1523.230.14194.2561976197192019200.971-0.0410.09360.1710.54994.898.394.898.394.81.6498.3
3.772-3.9433.370.16583.9764796479192219220.967-0.0250.10750.19860.56695.598.695.598.695.51.7198.6
3.626-3.7723.530.18313.867836783192119210.9630.0290.11350.21610.55295.498.795.498.795.41.898.7
3.5-3.6263.610.1963.5869386938192219220.9650.0210.120.23040.55995.798.595.798.595.71.8398.5
3.392-3.53.630.20893.3269696969192119210.9660.0460.12820.24580.5695.798.795.798.795.71.8498.7
3.292-3.3923.690.26132.7270807080192019200.9560.0160.15620.30490.5795.498.795.498.795.41.8998.7
3.204-3.2923.680.28612.5970707070192119210.9430.0650.17260.33480.5749396.39395.892.51.8896.3
3.113-3.2043.70.30152.5171027102192119210.934-0.0170.1820.35280.55288.390.888.385.182.81.8790.8
3.025-3.1133.670.3472.2770527052192219220.905-0.0430.20930.40610.5478588.28575.8731.8788.2
2.936-3.0253.710.38782.0971267126192119210.889-0.0440.23250.45290.55884.386.684.367.966.11.8886.6
2.844-2.9363.690.44191.8770927092192119210.869-0.0080.26680.51730.56881.784.181.75957.31.8784.1
2.735-2.8443.710.43031.9371327132192219220.8480.0410.25880.5030.56871.272.571.242.241.51.8772.5
2.576-2.7353.710.48461.7671367136192119210.821-0.0230.29270.56730.54161.662.561.624.123.71.8762.5
2.222-2.5763.740.50931.6671837183192119210.80.0580.30660.59550.5656.757.756.776.91.8957.7

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Processing

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

7shq


Resolution: 2.22→37.79 Å / SU ML: 0.2631 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 27.5874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 1912 4.98 %
Rwork0.2079 36487 -
obs0.209 38399 50.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.33 Å2
Refinement stepCycle: LAST / Resolution: 2.22→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8942 0 122 309 9373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229276
X-RAY DIFFRACTIONf_angle_d0.550812537
X-RAY DIFFRACTIONf_chiral_restr0.03961299
X-RAY DIFFRACTIONf_plane_restr0.00361636
X-RAY DIFFRACTIONf_dihedral_angle_d16.16473390
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.680268607746
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.677608570605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.37770.250385X-RAY DIFFRACTION1.69
2.28-2.340.190650.2977189X-RAY DIFFRACTION3.64
2.34-2.410.2806160.2475330X-RAY DIFFRACTION6.49
2.41-2.490.3124350.263520X-RAY DIFFRACTION10.2
2.49-2.570.252320.2635684X-RAY DIFFRACTION13.16
2.57-2.680.2827630.26441121X-RAY DIFFRACTION21.89
2.68-2.80.2639950.26491734X-RAY DIFFRACTION33.82
2.8-2.950.26871570.272857X-RAY DIFFRACTION55.65
2.95-3.130.27551760.25423783X-RAY DIFFRACTION72.95
3.13-3.370.26282200.22824837X-RAY DIFFRACTION93.2
3.37-3.710.22532820.20345082X-RAY DIFFRACTION98.53
3.71-4.250.21713180.18215035X-RAY DIFFRACTION98.56
4.25-5.350.1992320.17875139X-RAY DIFFRACTION98.99
5.35-37.790.2122740.19835091X-RAY DIFFRACTION99

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