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- PDB-1zyd: Crystal Structure of eIF2alpha Protein Kinase GCN2: Wild-Type Com... -

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Basic information

Entry
Database: PDB / ID: 1zyd
TitleCrystal Structure of eIF2alpha Protein Kinase GCN2: Wild-Type Complexed with ATP.
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 / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / ribosomal large subunit binding / 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 / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / negative regulation of translational initiation in response to stress / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / ribosomal large subunit binding / protein kinase inhibitor activity / translation initiation factor binding / cytosolic ribosome / cellular response to amino acid starvation / DNA damage checkpoint signaling / large ribosomal subunit / double-stranded RNA binding / ribosome binding / protein autophosphorylation / small ribosomal subunit / tRNA binding / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / translation / 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 profile. / RWD / RWD domain / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / : ...eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain profile. / RWD / RWD domain / 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) / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ADENOSINE-5'-TRIPHOSPHATE / eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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: Source and taxonomy / Category: entity_src_gen
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN ATP 303, MG 305, and MG 306 are associated with protein chain A ATP 304, MG 307, and MG ...HETEROGEN ATP 303, MG 305, and MG 306 are associated with protein chain A ATP 304, MG 307, and MG 308 are associated with protein chain B

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase GCN2
B: Serine/threonine-protein kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3998
Polymers70,2872
Non-polymers1,1126
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-48 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.110, 175.210, 47.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly of GCN2 protein kinase is a dimer. The asymmetric unit of this crystal lattice contains one dimer assembled into one biological unit.

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Components

#1: Protein Serine/threonine-protein kinase GCN2


Mass: 35143.477 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
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: 0.97931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 11, 2004
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 18487 / Num. obs: 18366 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.4
Reflection shellResolution: 2.75→2.81 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
CNX2000.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZXE

1zxe


Resolution: 2.75→47.59 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1390079.25 / 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
Rfree0.27 762 4.2 %SHELLS
Rwork0.208 ---
all0.208 18600 --
obs0.208 18323 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9052 Å2 / ksol: 0.35526 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2---15.06 Å20 Å2
3---13.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.75→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 66 68 4446
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.171.5
X-RAY DIFFRACTIONc_mcangle_it5.032
X-RAY DIFFRACTIONc_scbond_it4.412
X-RAY DIFFRACTIONc_scangle_it6.272.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 132 4.7 %
Rwork0.309 2675 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4atp_xplor_par.txtatp_xplor_top.txt

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