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- PDB-1ukx: Solution structure of the RWD domain of mouse GCN2 -

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Basic information

Entry
Database: PDB / ID: 1ukx
TitleSolution structure of the RWD domain of mouse GCN2
ComponentsGCN2 eIF2alpha kinase
KeywordsTRANSFERASE / eIF2alpha kinase / UBC-like fold / triple beta-turns / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / negative regulation of CREB transcription factor activity / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress ...regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / negative regulation of CREB transcription factor activity / regulation of translational initiation by eIF2 alpha phosphorylation / eiF2alpha phosphorylation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress / negative regulation by host of viral genome replication / regulation of translational initiation in response to stress / regulation of feeding behavior / T cell activation involved in immune response / positive regulation of adaptive immune response / regulation of translational initiation / cellular response to cold / neuron projection extension / negative regulation of neuron differentiation / long-term memory / cytosolic ribosome / endoplasmic reticulum unfolded protein response / negative regulation of translational initiation / positive regulation of defense response to virus by host / cellular response to amino acid starvation / cellular response to starvation / response to endoplasmic reticulum stress / learning / DNA damage checkpoint signaling / positive regulation of long-term synaptic potentiation / cellular response to UV / defense response to virus / adaptive immune response / viral translation / protein autophosphorylation / tRNA binding / negative regulation of translation / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Ubiquitin Conjugating Enzyme ...eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Anticodon-binding domain superfamily / Ubiquitin-conjugating enzyme/RWD-like / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsNameki, N. / Yoneyama, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2004
Title: Solution structure of the RWD domain of the mouse GCN2 protein.
Authors: Nameki, N. / Yoneyama, M. / Koshiba, S. / Tochio, N. / Inoue, M. / Seki, E. / Matsuda, T. / Tomo, Y. / Harada, T. / Saito, K. / Kobayashi, N. / Yabuki, T. / Aoki, M. / Nunokawa, E. / ...Authors: Nameki, N. / Yoneyama, M. / Koshiba, S. / Tochio, N. / Inoue, M. / Seki, E. / Matsuda, T. / Tomo, Y. / Harada, T. / Saito, K. / Kobayashi, N. / Yabuki, T. / Aoki, M. / Nunokawa, E. / Matsuda, N. / Sakagami, N. / Terada, T. / Shirouzu, M. / Yoshida, M. / Hirota, H. / Osanai, T. / Tanaka, A. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Kinoshita, K. / Guntert, P. / Kigawa, T. / Yokoyama, S.
History
DepositionSep 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN2 eIF2alpha kinase


Theoretical massNumber of molelcules
Total (without water)15,1521
Polymers15,1521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein GCN2 eIF2alpha kinase / GCN2


Mass: 15151.874 Da / Num. of mol.: 1 / Fragment: RWD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 2900069K12 / Plasmid: P021021-28
References: UniProt: Q9QZ05, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.0mM RWD domain U-15N, 13C, 20mM d-Tris-HCl, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Jhonson, B.A.data analysis
KUJIRA0.815Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
OPALpKoradi, R., Billeter, M., Guentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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