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- PDB-7shq: Structure of a functional construct of eukaryotic elongation fact... -

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Basic information

Entry
Database: PDB / ID: 7shq
TitleStructure of a functional construct of eukaryotic elongation factor 2 kinase in complex with calmodulin.
Components
  • Calmodulin-1
  • Eukaryotic elongation factor 2 kinase,Eukaryotic elongation factor 2 kinase
KeywordsTRANSLATION / elongation factor 2 kinase / eEF2 / Calmodulin
Function / homology
Function and homology information


elongation factor 2 kinase / elongation factor-2 kinase activity / response to prolactin / regulation of translation at postsynapse / regulation of protein autophosphorylation / myosin heavy chain kinase activity / myosin II filament disassembly / cellular response to anoxia / response to differentiation-inducing factor 1 / actomyosin contractile ring ...elongation factor 2 kinase / elongation factor-2 kinase activity / response to prolactin / regulation of translation at postsynapse / regulation of protein autophosphorylation / myosin heavy chain kinase activity / myosin II filament disassembly / cellular response to anoxia / response to differentiation-inducing factor 1 / actomyosin contractile ring / 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 / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 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 / translational elongation / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / mTORC1-mediated signalling / RHO GTPases activate PAKs / positive regulation of endocytosis / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / 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 / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to cAMP / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / cellular response to brain-derived neurotrophic factor stimulus / calcium channel complex / cellular response to calcium ion / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / response to ischemia / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / Stimuli-sensing channels
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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsPiserchio, A. / Isiorho, E.A. / Jeruzalmi, D. / Dalby, K.N. / Ghose, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084278 United States
Citation
Journal: Sci Adv / Year: 2022
Title: Structural basis for the calmodulin-mediated activation of eukaryotic elongation factor 2 kinase.
Authors: Piserchio, A. / Isiorho, E.A. / Long, K. / Bohanon, A.L. / Kumar, E.A. / Will, N. / Jeruzalmi, D. / Dalby, K.N. / Ghose, R.
#1: Journal: Biorxiv / Year: 2022
Title: Structural Basis for the Calmodulin-Mediated Activation of eEF-2K
Authors: Piserchio, A. / Isiorho, E.A. / Long, K. / Bohanon, A.L. / Kumar, E.A. / Will, N. / Jeruzalmi, D. / Dalby, K.N. / Ghose, R.
History
DepositionOct 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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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,Eukaryotic elongation factor 2 kinase
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,36910
Polymers77,1022
Non-polymers2678
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-80 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.495, 58.495, 365.779
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-322-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Eukaryotic elongation factor 2 kinase,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) / Gene: EEF2K / Production host: Escherichia coli (E. coli) / Strain (production host): BL210-DE3 / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DP23

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Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298.15 K / Method: microbatch / pH: 6.9
Details: Cocktail solution: Peg3350: 24% MgCl2: 300 mM BisTris pH 6.9: 100 mM Protein Solution: 11 mg/mL CaM-eEF2Kp1/1 Tris pH 7.5: 20 mM NaCl: 0.1 M CaCl2: 3mM TCEP: 1mM MgCl2: 1.5 mM AMPPNP: 1.0 mM ...Details: Cocktail solution: Peg3350: 24% MgCl2: 300 mM BisTris pH 6.9: 100 mM Protein Solution: 11 mg/mL CaM-eEF2Kp1/1 Tris pH 7.5: 20 mM NaCl: 0.1 M CaCl2: 3mM TCEP: 1mM MgCl2: 1.5 mM AMPPNP: 1.0 mM Crystallization conditions: 1/1 Protein/Cocktail under Paraffin Oil in a Greiner 72-Well microbatch plate
Temp details: Room temperature, not controlled

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.34→121.9 Å / Num. obs: 32010 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 14.98 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.073 / Rrim(I) all: 0.137 / Net I/σ(I): 14.5
Reflection shellResolution: 2.342→2.382 Å / Redundancy: 24.5 % / Rmerge(I) obs: 1.778 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1494 / CC1/2: 0.943 / Rpim(I) all: 0.368 / Rrim(I) all: 1.817 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
ISOLDE1.19.2_4158refinement
Coot0.9.5model building
MR-Rosetta1.19.2_4158phasing
autoPROC1.0.5data scaling
autoPROC1.0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV

3pdt

3lkm

4kuj

1ia9

6nx4

4ozs

3rjv


Resolution: 2.34→50.66 Å / SU ML: 0.2636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 1514 4.73 %
Rwork0.2293 30468 -
obs0.2304 31982 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.65 Å2
Refinement stepCycle: LAST / Resolution: 2.34→50.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 8 143 5257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345221
X-RAY DIFFRACTIONf_angle_d0.61147031
X-RAY DIFFRACTIONf_chiral_restr0.0412732
X-RAY DIFFRACTIONf_plane_restr0.0039932
X-RAY DIFFRACTIONf_dihedral_angle_d6.504694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.420.34371390.31372673X-RAY DIFFRACTION99.93
2.42-2.50.30171540.28292641X-RAY DIFFRACTION99.93
2.5-2.60.27691230.26512744X-RAY DIFFRACTION100
2.6-2.720.28141480.25772702X-RAY DIFFRACTION99.93
2.72-2.870.30931240.24932747X-RAY DIFFRACTION99.93
2.87-3.050.23161310.25312764X-RAY DIFFRACTION99.86
3.05-3.280.22341440.24382731X-RAY DIFFRACTION99.83
3.28-3.610.25361480.21532771X-RAY DIFFRACTION99.93
3.61-4.130.21821240.19912803X-RAY DIFFRACTION99.93
4.13-5.210.20831440.17832845X-RAY DIFFRACTION100
5.21-50.660.24151350.19793047X-RAY DIFFRACTION99.72

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