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- PDB-5ks5: Structure of the C-terminal Helical Repeat Domain of Elongation F... -

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Basic information

Entry
Database: PDB / ID: 5ks5
TitleStructure of the C-terminal Helical Repeat Domain of Elongation Factor 2 Kinase
ComponentsEukaryotic elongation factor 2 kinase
KeywordsTRANSFERASE / eEF2K / SEL1 / elongation / TPR
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 / translational elongation / mTORC1-mediated signalling / positive regulation of endocytosis / cellular response to cAMP / cellular response to brain-derived neurotrophic factor stimulus / cellular response to calcium ion / response to ischemia / cellular response to insulin stimulus / protein autophosphorylation / dendritic spine / postsynaptic density / calmodulin binding / protein kinase activity / glutamatergic synapse / calcium ion binding / negative regulation of apoptotic process / ATP binding / cytoplasm / cytosol
Similarity search - Function
Eukaryotic elongation factor 2 kinase / : / Sel1 repeat / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / Tetratricopeptide-like helical domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Eukaryotic elongation factor 2 kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsPiserchio, A. / Will, N. / Snyder, I. / Ferguson, S.B. / Giles, D.H. / Dalby, K.N. / Ghose, R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084278 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM059802 United States
Welch FoundationF-1390 United States
United States Department of Education GAANNP200A120211 United States
Alfred P. Sloan Foundation2014-6-25 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structure of the C-Terminal Helical Repeat Domain of Eukaryotic Elongation Factor 2 Kinase.
Authors: Will, N. / Piserchio, A. / Snyder, I. / Ferguson, S.B. / Giles, D.H. / Dalby, K.N. / Ghose, R.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 27, 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 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 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 1.5Jun 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 1.6May 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

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Assembly

Deposited unit
A: Eukaryotic elongation factor 2 kinase


Theoretical massNumber of molelcules
Total (without water)11,8561
Polymers11,8561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6870 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11856.014 Da / Num. of mol.: 1 / Fragment: UNP residues 627-725
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF2K / Plasmid: S3 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: O00418, elongation factor 2 kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1HNCO
121isotropic1HN(CA)CO
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic1H(CC)CONH
161isotropic1(H)CC(CO)NH
272isotropic43D (H)CCH-TOCSY
181isotropic43D 1H-15N NOESY
292isotropic23D 1H-13C NOESY aliphatic
1101isotropic33D 1H-15N NOESY aromatic
2112isotropic42D 1H-1H NOESY
1123anisotropic515N IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1600 uM [U-99% 13C; U-99% 15N] eEF2K_627-725, 50 mM sodium phosphate, 4 mM DTT, 95% H2O/5% D2OS3_H2O95% H2O/5% D2O
solution2300 uM [U-99% 13C; U-99% 15N] eEF2K_627-725, 50 mM sodium phosphate, 4 mM DTT, 100% D2OS3_D2O100% D2O
filamentous virus3300 uM [U-99% 13C; U-99% 1 eEF2K_627-725, 15 mg/mL Pf1 phage (ASLA Ltd), 50 mM sodium phosphate, 4 mM DTT, 90% H2O/10% D2OS3_RDC90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMeEF2K_627-725[U-99% 13C; U-99% 15N]1
50 mMsodium phosphatenatural abundance1
4 mMDTTnatural abundance1
300 uMeEF2K_627-725[U-99% 13C; U-99% 15N]2
50 mMsodium phosphatenatural abundance2
4 mMDTTnatural abundance2
300 uMeEF2K_627-725[U-99% 13C; U-99% 13
15 mg/mLPf1 phage (ASLA Ltd)natural abundance3
50 mMsodium phosphatenatural abundance3
4 mMDTTnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Temperature err
150 mM Sodium Phosphate mMH2O6.5 1 atm298.15 K0.2
250 mM Sodium Phosphate mMD2O6.5 pH*1 atm298.15 K0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCE IIIBrukerAVANCE III7003
Bruker AVANCEBrukerAVANCE8004
Bruker AVANCE IIIBrukerAVANCE III6005

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
ARIALinge, O'Donoghue and Nilgesrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
WHAT IFVrienddata analysis
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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