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- EMDB-44489: Cryo-EM Structure of GCN2 HRSL Domain -

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Basic information

Entry
Database: EMDB / ID: EMD-44489
TitleCryo-EM Structure of GCN2 HRSL Domain
Map data
Sample
  • Complex: GCN2 HRSL Domain
    • Protein or peptide: non-specific serine/threonine protein kinase
KeywordsKinase / Homodimer / Regulatory Domain / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation in response to stress / DNA damage checkpoint signaling / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity ...negative regulation of cytoplasmic translational initiation in response to stress / DNA damage checkpoint signaling / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSolorio-Kirpichyan KM / Golovenko D / Xiao F / Yan N / Korostelev AA / Korennykh AV
Funding support United States, France, 6 items
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 KM / Golovenko D / Xiao F / Yan N / Korostelev AA / Korennykh AV
History
DepositionApr 16, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44489.png

Downloads & links

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Map

FileDownload / File: emd_44489.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.16984165 - 0.45297754
Average (Standard dev.)0.004280999 (±0.017557615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44489_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44489_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GCN2 HRSL Domain

EntireName: GCN2 HRSL Domain
Components
  • Complex: GCN2 HRSL Domain
    • Protein or peptide: non-specific serine/threonine protein kinase

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Supramolecule #1: GCN2 HRSL Domain

SupramoleculeName: GCN2 HRSL Domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Kluyveromyces marxianus (yeast)
Molecular weightTheoretical: 116 KDa

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

MacromoleculeName: non-specific serine/threonine protein kinase / type: protein_or_peptide / ID: 1 / Details: Sequences for unresolved loops were deleted / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Kluyveromyces marxianus (yeast)
Molecular weightTheoretical: 190.970547 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSMSNLTLEQ YYEIQKLEME AIQSIYMDDF TDLTKRHSSW DKHPQIIFEV RLRSQESKPA ESSLDLHVVL PSTYPHASPQ ITFKHVVNV PDGQLNKVRK DIKEIHQRAK GQEIIYEIII AVQEILEDSQ KRVVTDSLED QRLQRIKDEE ERMKREEEQK L KQREKQKM ...String:
MSMSNLTLEQ YYEIQKLEME AIQSIYMDDF TDLTKRHSSW DKHPQIIFEV RLRSQESKPA ESSLDLHVVL PSTYPHASPQ ITFKHVVNV PDGQLNKVRK DIKEIHQRAK GQEIIYEIII AVQEILEDSQ KRVVTDSLED QRLQRIKDEE ERMKREEEQK L KQREKQKM QEQQYIDELF QKELAKRLDD DVADDNDKEI DLLPPPELTA SGQAFIFPRP ITAKLPNNSH YKFRAVIQPQ PI TLCDDPL SFANQMLVKP YIPAESPLYN VLKSSDKLDS IQYLLSEIIL DNPYFNTSNG KKEIALLEKD LESVLQVTHD NVC SLYAFH VERVGKNSAT FQWKIRLLTE YSQFNSLNDV VTSVGFVNLY TARGWILRLL EGLENLHKHG IAHKLIDMHT VQLT KDTDF GTTLPKFIHP SYGYSILSMI CRYPNKHGVK LEFPESKWTA PELIKFKGSK PQRKTDIWQL AVLFIVIITG VDTTL NYRS PGDFLESVEM DEALYDFLRK MLNPEPKQRL TPLELLPMKF LRTNIDPSWN KLNLYPDTSH SSRLLSNVAS SSGTQV LHS RTTSRASTDG GRRRSFNIGS RFSSLTSTSR SRYATDFEEI AVLGKGAYGQ VVKARNALDS RYYAIKKIRH SEEKLST IL SEVMLLASLN HRYVVRYYAA WLEEENSYTD SNAIDSDDDS STGSDLESDL DSDITRSSDG LSSRNRSLAH LNSNNWDF I SNSFQGSYPE IVFGNSSDED IEDGCDVSAS VDEKAGADST MDETEEKDNV TDMKFNKIKR QNGRFGSQKS SLKSTLFIQ MEYCENRTLY DLIHTESLNN QREEYWRLFR QILEALSYIH SQGIIHRDLK PMNIFIDESR NIKIGDFGLA KNVQKPQESL GRDSFASAG SSGDLTSAIG TALYVASEII TSHGNYNEKV DMYSLGVIFF EMIYPFDTGM ERVDVLKKLR SVDVEFPSDF D EKKLPTEK KIIRLLLDHD PTKRPSASAL LRSGWVPVKN QDELIKEALK NISDPSSPWQ QQVRESLFSQ PYHLSNDILF DL SRTDTTP FLQLLRAQMM DEVTKIFRRH GAIENNEPPM IFPKAPIYST QNVYEVLDRG GSVLQLQYDL TYPMARYLSK NPN TTSKQY RMQYVFRPSE SNHSSTEPRK FGEVDFDIIS NTTTDSAVHD AECLKVVDEI VSAFPVFTKT NVTLVLNHSD ILDG VFDFC NIDKAQRSLV SHMLSQLGFG KTFKDLKADL KTQLNISSTA LNDLELFDFK SDLDTAKKRL EKHLVDSPYL KRVEE ALVY ISKVVDYFKP LGVTRNVVIA PLSNYNNGFY KGGLMFQSVF DSGRSRSLIS AGGRYDNLIS LIARPSGGKL NHIQKA VGF NLAWETMFLI VKNYFKLAGG RSTKKISKGL KLTNSEWKPK RCEVLISSFS NSLLNTIGIE VISKLWKAGI SADIVRD CF SVEDVITAAQ KDGVDWIVLI KQQNYSISNN KRRYKPFKVK NLSSNLDSDM DFEEFLLTYE DSFSKDSTND SMNKEDYF N EYDDRNRWDD NSSQERSQDG ETDNLSSNGP QKVIYIPNPA TRAKGKPSKK DKWVYEESAR NASKQLIHSL SSVPIFAVD AIRDETLEII SITSLAQKDE WLRKVFGSAA NSAPRSFATS IYNNLSKEAA KGGRWAIVHC NKTGKSCVVD LQR

UniProtKB: non-specific serine/threonine protein kinase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
350.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris
2.0 mMMgCl2magnesium chloride
5.0 mMC4H10O2S2DTT
0.1 %Triton-x 100
1.0 %C3H8O3Glycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9048 / Average exposure time: 5.9 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1697401
CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 215101
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 185957 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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