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- EMDB-41094: CryoEM structure of the HisRS-like domain of human GCN2 -

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Basic information

Entry
Database: EMDB / ID: EMD-41094
TitleCryoEM structure of the HisRS-like domain of human GCN2
Map datamain map from homogeneous refinement non sharpened
Sample
  • Complex: dimeric HisRS-like domain of human GCN2
    • Protein or peptide: eIF-2-alpha kinase GCN2
KeywordsGCN2 / HisRS / pseudoenzyme / translation / TRANSFERASE
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 / defense response to virus / viral translation / tRNA binding / adaptive immune response / protein autophosphorylation / 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
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin JZ / Keszei AFA / Mazhab-Jafari MT / Sicheri F
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: CryoEM structure of the HisRS-like domain of human GCN2
Authors: Yin JZ / Keszei AFA / Mazhab-Jafari MT / Sicheri F
History
DepositionJun 21, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41094.png

Downloads & links

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Map

FileDownload / File: emd_41094.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map from homogeneous refinement non sharpened
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.42584234 - 1.0154661
Average (Standard dev.)0.00046816628 (±0.028361958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41094_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_41094_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: additional map from non uniform refinement non sharpened

Fileemd_41094_additional_1.map
Annotationadditional map from non uniform refinement non sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A of main map from homogeneous refinement

Fileemd_41094_half_map_1.map
Annotationhalf map A of main map from homogeneous refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of main map from homogeneous refinement

Fileemd_41094_half_map_2.map
Annotationhalf map B of main map from homogeneous refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimeric HisRS-like domain of human GCN2

EntireName: dimeric HisRS-like domain of human GCN2
Components
  • Complex: dimeric HisRS-like domain of human GCN2
    • Protein or peptide: eIF-2-alpha kinase GCN2

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Supramolecule #1: dimeric HisRS-like domain of human GCN2

SupramoleculeName: dimeric HisRS-like domain of human GCN2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: eIF-2-alpha kinase GCN2

MacromoleculeName: eIF-2-alpha kinase GCN2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 187.216578 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GMAGGRGAPG RGRDEPPESY PQRQDHELQA LEAIYGADFQ DLRPDACGPV KEPPEINLVL YPQGLTGEEV YVKVDLRVKC PPTYPDVVP EIELKNAKGL SNESVNLLKS RLEELAKKHC GEVMIFELAY HVQSFLSEHN KPPPKSFHEE MLERRAQEEQ Q RLLEAKRK ...String:
GMAGGRGAPG RGRDEPPESY PQRQDHELQA LEAIYGADFQ DLRPDACGPV KEPPEINLVL YPQGLTGEEV YVKVDLRVKC PPTYPDVVP EIELKNAKGL SNESVNLLKS RLEELAKKHC GEVMIFELAY HVQSFLSEHN KPPPKSFHEE MLERRAQEEQ Q RLLEAKRK EEQEQREILH EIQRRKEEIK EEKKRKEMAK QERLEIASLS NQDHTSKKDP GGHRTAAILH GGSPDFVGNG KH RANSSGR SRRERQYSVC NSEDSPGSCE ILYFNMGSPD QLMVHKGKCI GSDEQLGKLV YNALETATGG FVLLYEWVLQ WQK KMGPFL TSQEKEKIDK CKKQIQGTET EFNSLVKLSH PNVVRYLAMN LKEQDDSIVV DILVEHISGV SLAAHLSHSG PIPV HQLRR YTAQLLSGLD YLHSNSVVHK VLSASNVLVD AEGTVKITDY SISKRLADIC KEDVFEQTRV RFSDNALPYK TGKKG DVWR LGLLLLSLSQ GQECGEYPVT IPSDLPADFQ DFLKKCVCLD DKERWSPQQL LKHSFINPQP KMPLVEQSPE DSEGQD YVE TVIPSNRLPS AAFFSETQRQ FSRYFIEFEE LQLLGKGAFG AVIKVQNKLD GCCYAVKRIP INPASRQFRR IKGEVTL LS RLHHENIVRY YNAWIERHER PAGPGTPPPD SGPLAKDDRA ARGQPASDTD GLDSVEAAAP PPILSSSVEW STSGERSA S ARFPATGPGS SDDEDDDEDE HGGVFSQSFL PASDSESDII FDNEDENSKS QNQDEDCNEK NGCHESEPSV TTEAVHYLY IQMEYCEKST LRDTIDQGLY RDTVRLWRLF REILDGLAYI HEKGMIHRDL KPVNIFLDSD DHVKIGDFGL ATDHLAFSAD SKQDDQTGD LIKSDPSGHL TGMVGTALYV SPEVQGSTKS AYNQKVDLFS LGIIFFEMSY HPMVTASERI FVLNQLRDPT S PKFPEDFD DGEHAKQKSV ISWLLNHDPA KRPTATELLK SELLPPPQME ESELHEVLHH TLTNVDGKAY RTMMAQIFSQ RI SPAIDYT YDSDILKGNF SIRTAKMQQH VCETIIRIFK RHGAVQLCTP LLLPRNRQIY EHNEAALFMD HSGMLVMLPF DLR IPFARY VARNNILNLK RYCIERVFRP RKLDRFHPKE LLECAFDIVT STTNSFLPTA EIIYTIYEII QEFPALQERN YSIY LNHTM LLKAILLHCG IPEDKLSQVY IILYDAVTEK LTRREVEAKF CNLSLSSNSL CRLYKFIEQK GDLQDLMPTI NSLIK QKTG IAQLVKYGLK DLEEVVGLLK KLGIKLQVLI NLGLVYKVQQ HNGIIFQFVA FIKRRQRAVP EILAAGGRYD LLIPQF RGP QALGPVPTAI GVSIAIDKIS AAVLNMEESV TISSCDLLVV SVGQMSMSRA INLTQKLWTA GITAEIMYDW SQSQEEL QE YCRHHEITYV ALVSDKEGSH VKVKSFEKER QTEKRVLETE LVDHVLQKLR TKVTDERNGR EASDNLAVQN LKGSFSNA S GLFEIHGATV VPIVSVLAPE KLSASTRRRY ETQVQTRLQT SLANLHQKSS EIEILAVDLP KETILQFLSL EWDADEQAF NTTVKQLLSR LPKQRYLKLV CDEIYNIKVE KKVSVLFLYS YRDDYYRILF

UniProtKB: eIF-2-alpha kinase GCN2

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 229225
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8t7t:
CryoEM structure of the HisRS-like domain of human GCN2

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