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- PDB-7qq6: GCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 1 (dovi... -

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Basic information

Entry
Database: PDB / ID: 7qq6
TitleGCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 1 (dovitinib)
ComponentseIF-2-alpha kinase GCN2
KeywordsTRANSFERASE / EIF2 kinase / Integrated Stress Response / GCN2
Function / homology
Function and homology information


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 / 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 feeding behavior ...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 / 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 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 / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of neuron differentiation / long-term memory / negative regulation of translational initiation / positive regulation of defense response to virus by host / cellular response to amino acid starvation / cytosolic ribosome / DNA damage checkpoint signaling / learning / positive regulation of long-term synaptic potentiation / cellular response to UV / viral translation / defense response to virus / tRNA binding / protein autophosphorylation / adaptive immune response / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase 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) / 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
Similarity search - Domain/homology
Chem-38O / eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMaia de Oliveira, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Biochem.J. / Year: 2020
Title: The structure of human GCN2 reveals a parallel, back-to-back kinase dimer with a plastic DFG activation loop motif.
Authors: Maia de Oliveira, T. / Korboukh, V. / Caswell, S. / Winter Holt, J.J. / Lamb, M. / Hird, A.W. / Overman, R.
History
DepositionJan 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eIF-2-alpha kinase GCN2
B: eIF-2-alpha kinase GCN2
C: eIF-2-alpha kinase GCN2
D: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7088
Polymers147,1394
Non-polymers1,5704
Water81145
1
A: eIF-2-alpha kinase GCN2
B: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3544
Polymers73,5692
Non-polymers7852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: eIF-2-alpha kinase GCN2
D: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3544
Polymers73,5692
Non-polymers7852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.420, 162.600, 123.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1808-

HOH

21A-1812-

HOH

31B-1810-

HOH

41B-1812-

HOH

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Components

#1: Protein
eIF-2-alpha kinase GCN2 / Eukaryotic translation initiation factor 2-alpha kinase 4 / GCN2-like protein


Mass: 36784.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK4, GCN2, KIAA1338 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P2K8, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-38O / 4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one / Dovitinib / Fibroblast growth factor receptor 1


Mass: 392.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H21FN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH6 with 20 per cent PEG 8000 and 200mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.97857 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.79→49.36 Å / Num. obs: 38997 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 92 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.7
Reflection shellResolution: 2.79→2.87 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.674 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 17912 / % possible all: 94.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYD

1zyd


Resolution: 2.8→24.64 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.854 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.759 / SU Rfree Blow DPI: 0.331 / SU Rfree Cruickshank DPI: 0.341
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1946 5 %RANDOM
Rwork0.211 ---
obs0.213 38918 99.7 %-
Displacement parametersBiso max: 200.82 Å2 / Biso mean: 91.21 Å2 / Biso min: 45.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.238 Å20 Å20 Å2
2---11.3141 Å20 Å2
3---12.5521 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.8→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8531 0 116 45 8692
Biso mean--85.3 75.47 -
Num. residues----1071
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3023SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1473HARMONIC5
X-RAY DIFFRACTIONt_it8866HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1131SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9838SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8866HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12033HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion21.86
LS refinement shellResolution: 2.8→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.5514 39 5.01 %
Rwork0.3738 740 -
all0.3822 779 -
obs--85.52 %

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