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- PDB-1zyc: Crystal Structure of eIF2alpha Protein Kinase GCN2: Wild-Type in ... -

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Basic information

Entry
Database: PDB / ID: 1zyc
TitleCrystal Structure of eIF2alpha Protein Kinase GCN2: Wild-Type in Apo Form.
ComponentsSerine/threonine-protein kinase GCN2
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 / large ribosomal subunit / double-stranded RNA binding / 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 / MOLECULAR REPLACEMENT / Resolution: 3 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 9, 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: Version format compliance
Revision 1.3Aug 2, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase GCN2
B: Serine/threonine-protein kinase GCN2
C: Serine/threonine-protein kinase GCN2
D: Serine/threonine-protein kinase GCN2


Theoretical massNumber of molelcules
Total (without water)140,5744
Polymers140,5744
Non-polymers00
Water25214
1
A: Serine/threonine-protein kinase GCN2
B: Serine/threonine-protein kinase GCN2


Theoretical massNumber of molelcules
Total (without water)70,2872
Polymers70,2872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-8 kcal/mol
Surface area25040 Å2
MethodPISA
2
C: Serine/threonine-protein kinase GCN2
D: Serine/threonine-protein kinase GCN2


Theoretical massNumber of molelcules
Total (without water)70,2872
Polymers70,2872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-7 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.890, 95.700, 175.120
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 two dimers assembled into two biological dimer units as chains (AB) and (CD), respectively.

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Components

#1: Protein
Serine/threonine-protein kinase GCN2


Mass: 35143.477 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG 3350, CHES, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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 29, 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: 3→50 Å / Num. all: 26813 / Num. obs: 26187 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 92.2

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Processing

Software
NameVersionClassification
CNX2000.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZXE

1zxe


Resolution: 3→41.99 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 681876.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 562 2.2 %SHELLS
Rwork0.234 ---
all0.234 27608 --
obs0.234 26099 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2173 Å2 / ksol: 0.350518 e/Å3
Displacement parametersBiso mean: 75.4 Å2
Baniso -1Baniso -2Baniso -3
1--20.22 Å20 Å20 Å2
2--37.81 Å20 Å2
3----17.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8587 0 0 14 8601
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.471.5
X-RAY DIFFRACTIONc_mcangle_it5.572
X-RAY DIFFRACTIONc_scbond_it4.922
X-RAY DIFFRACTIONc_scangle_it7.032.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.457 90 2.2 %
Rwork0.391 4037 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3&_1_TOPOLOGY_INFILE_3

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