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- PDB-1zxe: Crystal Structure of eIF2alpha Protein Kinase GCN2: D835N Inactiv... -

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Basic information

Entry
Database: PDB / ID: 1zxe
TitleCrystal Structure of eIF2alpha Protein Kinase GCN2: D835N Inactivating Mutant in Apo Form
ComponentsSerine/threonine-protein kinaseSerine/threonine-specific protein kinase
KeywordsTRANSFERASE / Translation regulator / Protein kinase / Signal transduction / Amino-acid starvation / Starvation stress response / eIF2alpha kinase
Function / homology
Function and homology information


cellular response to histidine / 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 / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / : / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity ...cellular response to histidine / 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 / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / : / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding / translation initiation factor binding / cellular response to amino acid starvation / cytosolic ribosome / DNA damage checkpoint signaling / : / ribosome binding / double-stranded RNA binding / large ribosomal subunit / small ribosomal subunit / tRNA binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / translation / protein phosphorylation / protein serine kinase activity / protein homodimerization activity / ATP binding / nucleus / cytosol / cytoplasm
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 / Anticodon-binding domain superfamily ...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 / Anticodon-binding domain superfamily / Ubiquitin-conjugating enzyme/RWD-like / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsPadyana, A.K. / Qiu, H. / Roll-Mecak, A. / Hinnebusch, A.G. / Burley, S.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Basis for Autoinhibition and Mutational Activation of Eukaryotic Initiation Factor 2{alpha} Protein Kinase GCN2
Authors: Padyana, A.K. / Qiu, H. / Roll-Mecak, A. / Hinnebusch, A.G. / Burley, S.K.
History
DepositionJun 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 600HETEROGEN GOL 398 is associated with protein chain A. GOL 498 is associated with protein chain B. ...HETEROGEN GOL 398 is associated with protein chain A. GOL 498 is associated with protein chain B. GOL 598 is associated with protein chain C. GOL 698 is associated with protein chain D. GOL 798 is associated with protein chain E. GOL 898 is associated with protein chain F.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase
B: Serine/threonine-protein kinase
C: Serine/threonine-protein kinase
D: Serine/threonine-protein kinase
E: Serine/threonine-protein kinase
F: Serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,94012
Polymers213,3876
Non-polymers5536
Water5,026279
1
A: Serine/threonine-protein kinase
B: Serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3134
Polymers71,1292
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-13 kcal/mol
Surface area25160 Å2
MethodPISA
2
C: Serine/threonine-protein kinase
D: Serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3134
Polymers71,1292
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-12 kcal/mol
Surface area25740 Å2
MethodPISA
3
E: Serine/threonine-protein kinase
F: Serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3134
Polymers71,1292
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-10 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.560, 154.140, 157.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly of GCN2 protein kinase is a dimer. The asymmetric unit of this crystal lattice contains three dimers. They are grouped via chain IDs into (AB), (CD), and (EF) as dimers.

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Components

#1: Protein
Serine/threonine-protein kinase / Serine/threonine-specific protein kinase


Mass: 35564.543 Da / Num. of mol.: 6 / Mutation: D835N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCN2, AAS1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: P15442, EC: 2.7.1.37
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.4
Details: PEG3350, CAPSO, pH 9.4, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97935 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 31, 2004
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 59995 / Num. obs: 59469 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.6
Reflection shellResolution: 2.6→2.66 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.5 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CNX2000.1refinement
MAR345data collection
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→35.35 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3021353.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1206 2 %SHELLS
Rwork0.204 ---
all0.204 59469 --
obs0.204 59414 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8098 Å2 / ksol: 0.34526 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å20 Å20 Å2
2---2.26 Å20 Å2
3---7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12927 0 36 279 13242
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.461.5
X-RAY DIFFRACTIONc_mcangle_it4.942
X-RAY DIFFRACTIONc_scbond_it5.222
X-RAY DIFFRACTIONc_scangle_it6.792.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 166 1.7 %
Rwork0.29 9475 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2GOL_par.txt&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.param&_1_TOPOLOGY_INFILE_3

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