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- PDB-7qwk: GCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 2 -

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Basic information

Entry
Database: PDB / ID: 7qwk
TitleGCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 2
ComponentseIF-2-alpha kinase GCN2
KeywordsTRANSFERASE / GCN2 / EIF2 kinase / ISR / Integrated Stress Response
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 / positive regulation of adaptive immune response / T cell activation involved in 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 / positive regulation of defense response to virus by host / negative regulation of translational initiation / cytosolic ribosome / cellular response to amino acid starvation / DNA damage checkpoint signaling / learning / positive regulation of long-term synaptic potentiation / cellular response to UV / defense response to virus / viral translation / protein autophosphorylation / adaptive immune response / tRNA binding / non-specific serine/threonine protein kinase / 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 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) / 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-G41 / eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaia de Oliveira, T.
Funding support1items
OrganizationGrant numberCountry
Other private
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 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 2.0Jul 12, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / diffrn_source ...atom_site / diffrn_source / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _diffrn_source.pdbx_synchrotron_site ..._atom_site.label_seq_id / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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
E: eIF-2-alpha kinase GCN2
F: eIF-2-alpha kinase GCN2
G: eIF-2-alpha kinase GCN2
H: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,90118
Polymers293,1248
Non-polymers3,77710
Water1,51384
1
A: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0932
Polymers36,6411
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0932
Polymers36,6411
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0932
Polymers36,6411
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0932
Polymers36,6411
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0932
Polymers36,6411
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0932
Polymers36,6411
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0932
Polymers36,6411
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: eIF-2-alpha kinase GCN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2494
Polymers36,6411
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.799, 77.795, 101.690
Angle α, β, γ (deg.)89.860, 90.050, 68.580
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 36640.512 Da / Num. of mol.: 8
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-G41 / (2~{S})-~{N}-[(1~{S})-1-[4-[(6-pyridin-4-ylquinazolin-2-yl)amino]phenyl]ethyl]piperidine-2-carboxamide


Mass: 452.551 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H28N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Bis Tris, 20 to 30 percent PEG3350, 200mM ammonium sulfate
PH range: 5.5-6.5 / Temp details: 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→42.67 Å / Num. obs: 90485 / % possible obs: 96.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 44.58 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 3.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3929 / % possible all: 85

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYD

1zyd


Resolution: 2.3→42 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.243 --RANDOM
Rwork0.214 ---
obs-90484 96 %-
Displacement parametersBiso max: 147.42 Å2 / Biso mean: 50.4159 Å2 / Biso min: 18.87 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15636 0 280 84 16000

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