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- PDB-9bf3: Cryo-EM Structure of GCN2 HRSL Domain -

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Basic information

Entry
Database: PDB / ID: 9bf3
TitleCryo-EM Structure of GCN2 HRSL Domain
Componentsnon-specific serine/threonine protein kinase
KeywordsSIGNALING PROTEIN / Kinase / Homodimer / Regulatory Domain
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation in response to stress / positive regulation of metabolic process / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / DNA damage checkpoint signaling / tRNA binding / non-specific serine/threonine protein kinase / ATP binding / nucleus / cytosol
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
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSolorio-Kirpichyan, K.M. / Golovenko, D. / Xiao, F. / Yan, N. / Korostelev, A.A. / Korennykh, A.V.
Funding support United States, France, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM110161-01 United States
Burroughs Wellcome FundAWD1004002 United States
The Vallee Foundation Inc.1013579 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007388 United States
Human Frontier Science Program (HFSP)LT000754 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127094 United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of GCN2 HisRS-Like Domain
Authors: Solorio-Kirpichyan, K.M. / Golovenko, D. / Xiao, F. / Yan, N. / Korostelev, A.A. / Korennykh, A.V.
History
DepositionApr 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
B: non-specific serine/threonine protein kinase


Theoretical massNumber of molelcules
Total (without water)381,9412
Polymers381,9412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1000 - 1507 / Label seq-ID: 1000 - 1507

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999999116187, -0.000421745301729, 0.00126085519001), (0.000422428043447, -0.999999764289, 0.000541273721841), (0.00126062661316, 0.000541805864047, 0.999999058633) ...NCS oper: (Code: given
Matrix: (-0.999999116187, -0.000421745301729, 0.00126085519001), (0.000422428043447, -0.999999764289, 0.000541273721841), (0.00126062661316, 0.000541805864047, 0.999999058633)
Vector: 207.938595645, 207.899653466, -0.187441765035)

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Components

#1: Protein non-specific serine/threonine protein kinase


Mass: 190970.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequences for unresolved loops were deleted / Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Gene: GCN2, KLMA_30413
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: W0T9H7, non-specific serine/threonine protein kinase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GCN2 HRSL Domain / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.116 MDa / Experimental value: NO
Source (natural)Organism: Kluyveromyces marxianus (yeast)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1350 mMsodium chlorideNaCl1
220 mMTrisC4H11NO31
32 mMmagnesium chlorideMgCl21
45 mMDTTC4H10O2S21
50.1 %Triton-x 1001
61 %GlycerolC3H8O31
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / C2 aperture diameter: 100 µm
Image recordingAverage exposure time: 5.9 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9048

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.1particle selection
2EPU2.14image acquisitionEPU 2.14 was used to collect images
8PHENIXmodel refinement
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1697401
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215101 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 118.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00227958
ELECTRON MICROSCOPYf_angle_d0.421510760
ELECTRON MICROSCOPYf_chiral_restr0.03821206
ELECTRON MICROSCOPYf_plane_restr0.00541378
ELECTRON MICROSCOPYf_dihedral_angle_d3.05881044
Refine LS restraints NCSType: NCS constraints / Rms dev position: 1.92267504883E-10 Å

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