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- EMDB-32023: eIF2B-SFSV NSs C2-imposed -

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Basic information

Entry
Database: EMDB / ID: EMD-32023
TitleeIF2B-SFSV NSs C2-imposed
Map data
Sample
  • Complex: Complex of human eIF2B with SFSV NSs protein
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF-2B subunit epsilon
    • Protein or peptide: Non-structural protein NS-S
KeywordsComplex / TRANSLATION
Function / homology
Function and homology information


eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / guanyl-nucleotide exchange factor complex / astrocyte development / astrocyte differentiation / regulation of translational initiation / positive regulation of translational initiation / response to glucose ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / guanyl-nucleotide exchange factor complex / astrocyte development / astrocyte differentiation / regulation of translational initiation / positive regulation of translational initiation / response to glucose / ovarian follicle development / translation initiation factor binding / translational initiation / translation initiation factor activity / myelination / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / central nervous system development / hippocampus development / response to peptide hormone / regulation of translation / T cell receptor signaling pathway / response to heat / positive regulation of apoptotic process / GTP binding / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like / Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / eIF4-gamma/eIF5/eIF2-epsilon ...Phlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like / Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Armadillo-type fold
Similarity search - Domain/homology
Non-structural protein NS-S / Translation initiation factor eIF2B subunit beta / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit alpha / Translation initiation factor eIF2B subunit gamma / Translation initiation factor eIF2B subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human) / Sandfly fever sicilian virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsKashiwagi K / Ito T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Commun / Year: 2021
Title: eIF2B-capturing viral protein NSs suppresses the integrated stress response.
Authors: Kazuhiro Kashiwagi / Yuichi Shichino / Tatsuya Osaki / Ayako Sakamoto / Madoka Nishimoto / Mari Takahashi / Mari Mito / Friedemann Weber / Yoshiho Ikeuchi / Shintaro Iwasaki / Takuhiro Ito /
Abstract: Various stressors such as viral infection lead to the suppression of cap-dependent translation and the activation of the integrated stress response (ISR), since the stress-induced phosphorylated ...Various stressors such as viral infection lead to the suppression of cap-dependent translation and the activation of the integrated stress response (ISR), since the stress-induced phosphorylated eukaryotic translation initiation factor 2 [eIF2(αP)] tightly binds to eIF2B to prevent it from exchanging guanine nucleotide molecules on its substrate, unphosphorylated eIF2. Sandfly fever Sicilian virus (SFSV) evades this cap-dependent translation suppression through the interaction between its nonstructural protein NSs and host eIF2B. However, its precise mechanism has remained unclear. Here, our cryo-electron microscopy (cryo-EM) analysis reveals that SFSV NSs binds to the α-subunit of eIF2B in a competitive manner with eIF2(αP). Together with SFSV NSs, eIF2B retains nucleotide exchange activity even in the presence of eIF2(αP), in line with the cryo-EM structures of the eIF2B•SFSV NSs•unphosphorylated eIF2 complex. A genome-wide ribosome profiling analysis clarified that SFSV NSs expressed in cultured human cells attenuates the ISR triggered by thapsigargin, an endoplasmic reticulum stress inducer. Furthermore, SFSV NSs introduced in rat hippocampal neurons and human induced-pluripotent stem (iPS) cell-derived motor neurons exhibits neuroprotective effects against the ISR-inducing stress. Since ISR inhibition is beneficial in various neurological disease models, SFSV NSs may be a promising therapeutic ISR inhibitor.
History
DepositionOct 4, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vlk
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vlk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32023.png

Downloads & links

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Map

FileDownload / File: emd_32023.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.829 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 5
Minimum - Maximum-22.302153000000001 - 43.820605999999998
Average (Standard dev.)0.000000000004658 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8290.8290.829
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z331.600331.600331.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-22.30243.8210.000

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Supplemental data

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Sample components

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Entire : Complex of human eIF2B with SFSV NSs protein

EntireName: Complex of human eIF2B with SFSV NSs protein
Components
  • Complex: Complex of human eIF2B with SFSV NSs protein
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF-2B subunit epsilon
    • Protein or peptide: Non-structural protein NS-S

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Supramolecule #1: Complex of human eIF2B with SFSV NSs protein

SupramoleculeName: Complex of human eIF2B with SFSV NSs protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: Translation initiation factor eIF-2B subunit alpha

MacromoleculeName: Translation initiation factor eIF-2B subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.908316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMDDKELIE YFKSQMKEDP DMASAVAAIR TLLEFLKRDK GETIQGLRAN LTSAIETLCG VDSSVAVSSG GELFLRFISL ASLEYSDYS KCKKIMIERG ELFLRRISLS RNKIADLCHT FIKDGATILT HAYSRVVLRV LEAAVAAKKR FSVYVTESQP D LSGKKMAK ...String:
GPMDDKELIE YFKSQMKEDP DMASAVAAIR TLLEFLKRDK GETIQGLRAN LTSAIETLCG VDSSVAVSSG GELFLRFISL ASLEYSDYS KCKKIMIERG ELFLRRISLS RNKIADLCHT FIKDGATILT HAYSRVVLRV LEAAVAAKKR FSVYVTESQP D LSGKKMAK ALCHLNVPVT VVLDAAVGYI MEKADLVIVG AEGVVENGGI INKIGTNQMA VCAKAQNKPF YVVAESFKFV RL FPLNQQD VPDKFKYKAD TLKVAQTGQD LKEEHPWVDY TAPSLITLLF TDLGVLTPSA VSDELIKLYL

UniProtKB: Translation initiation factor eIF2B subunit alpha

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Macromolecule #2: Translation initiation factor eIF-2B subunit beta

MacromoleculeName: Translation initiation factor eIF-2B subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.039547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPGSAAKGSE LSERIESFVE TLKRGGGPRS SEEMARETLG LLRQIITDHR WSNAGELMEL IRREGRRMTA AQPSETTVGN MVRRVLKII REEYGRLHGR SDESDQQESL HKLLTSGGLN EDFSFHYAQL QSNIIEAINE LLVELEGTME NIAAQALEHI H SNEVIMTI ...String:
MPGSAAKGSE LSERIESFVE TLKRGGGPRS SEEMARETLG LLRQIITDHR WSNAGELMEL IRREGRRMTA AQPSETTVGN MVRRVLKII REEYGRLHGR SDESDQQESL HKLLTSGGLN EDFSFHYAQL QSNIIEAINE LLVELEGTME NIAAQALEHI H SNEVIMTI GFSRTVEAFL KEAARKRKFH VIVAECAPFC QGHEMAVNLS KAGIETTVMT DAAIFAVMSR VNKVIIGTKT IL ANGALRA VTGTHTLALA AKHHSTPLIV CAPMFKLSPQ FPNEEDSFHK FVAPEEVLPF TEGDILEKVS VHCPVFDYVP PEL ITLFIS NIGGNAPSYI YRLMSELYHP DDHVL

UniProtKB: Translation initiation factor eIF2B subunit beta

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Macromolecule #3: Translation initiation factor eIF-2B subunit gamma

MacromoleculeName: Translation initiation factor eIF-2B subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.30423 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEFQAVVMAV GGGSRMTDLT SSIPKPLLPV GNKPLIWYPL NLLERVGFEE VIVVTTRDVQ KALCAEFKMK MKPDIVCIPD DADMGTADS LRYIYPKLKT DVLVLSCDLI TDVALHEVVD LFRAYDASLA MLMRKGQDSI EPVPGQKGKK KAVEQRDFIG V DSTGKRLL ...String:
MEFQAVVMAV GGGSRMTDLT SSIPKPLLPV GNKPLIWYPL NLLERVGFEE VIVVTTRDVQ KALCAEFKMK MKPDIVCIPD DADMGTADS LRYIYPKLKT DVLVLSCDLI TDVALHEVVD LFRAYDASLA MLMRKGQDSI EPVPGQKGKK KAVEQRDFIG V DSTGKRLL FMANEADLDE ELVIKGSILQ KHPRIRFHTG LVDAHLYCLK KYIVDFLMEN GSITSIRSEL IPYLVRKQFS SA SSQQGQE EKEEDLKKKE LKSLDIYSFI KEANTLNLAP YDACWNACRG DRWEDLSRSQ VRCYVHIMKE GLCSRVSTLG LYM EANRQV PKLLSALCPE EPPVHSSAQI VSKHLVGVDS LIGPETQIGE KSSIKRSVIG SSCLIKDRVT ITNCLLMNSV TVEE GSNIQ GSVICNNAVI EKGADIKDCL IGSGQRIEAK AKRVNEVIVG NDQLMEI

UniProtKB: Translation initiation factor eIF2B subunit gamma

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Macromolecule #4: Translation initiation factor eIF-2B subunit delta

MacromoleculeName: Translation initiation factor eIF-2B subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.640168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAVAVAVRE DSGSGMKAEL PPGPGAVGRE MTKEEKLQLR KEKKQQKKKR KEEKGAEPET GSAVSAAQCQ VGPTRELPES GIQLGTPRE KVPAGRSKAE LRAERRAKQE AERALKQARK GEQGGPPPKA SPSTAGETPS GVKRLPEYPQ VDDLLLRRLV K KPERQQVP ...String:
MAAVAVAVRE DSGSGMKAEL PPGPGAVGRE MTKEEKLQLR KEKKQQKKKR KEEKGAEPET GSAVSAAQCQ VGPTRELPES GIQLGTPRE KVPAGRSKAE LRAERRAKQE AERALKQARK GEQGGPPPKA SPSTAGETPS GVKRLPEYPQ VDDLLLRRLV K KPERQQVP TRKDYGSKVS LFSHLPQYSR QNSLTQFMSI PSSVIHPAMV RLGLQYSQGL VSGSNARCIA LLRALQQVIQ DY TTPPNEE LSRDLVNKLK PYMSFLTQCR PLSASMHNAI KFLNKEITSV GSSKREEEAK SELRAAIDRY VQEKIVLAAQ AIS RFAYQK ISNGDVILVY GCSSLVSRIL QEAWTEGRRF RVVVVDSRPW LEGRHTLRSL VHAGVPASYL LIPAASYVLP EVSK VLLGA HALLANGSVM SRVGTAQLAL VARAHNVPVL VCCETYKFCE RVQTDAFVSN ELDDPDDLQC KRGEHVALAN WQNHA SLRL LNLVYDVTPP ELVDLVITEL GMIPCSSVPV VLRVKSSDQ

UniProtKB: Translation initiation factor eIF2B subunit delta

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Macromolecule #5: Translation initiation factor eIF-2B subunit epsilon

MacromoleculeName: Translation initiation factor eIF-2B subunit epsilon / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.466609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS KDQPRVLLPL ANVALIDYTL EFLTATGVQ ETFVFCCWKA AQIKEHLLKS KWCRPTSLNV VRIITSELYR SLGDVLRDVD AKALVRSDFL LVYGDVISNI N ITRALEEH ...String:
MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS KDQPRVLLPL ANVALIDYTL EFLTATGVQ ETFVFCCWKA AQIKEHLLKS KWCRPTSLNV VRIITSELYR SLGDVLRDVD AKALVRSDFL LVYGDVISNI N ITRALEEH RLRRKLEKNV SVMTMIFKES SPSHPTRCHE DNVVVAVDST TNRVLHFQKT QGLRRFAFPL SLFQGSSDGV EV RYDLLDC HISICSPQVA QLFTDNFDYQ TRDDFVRGLL VNEEILGNQI HMHVTAKEYG ARVSNLHMYS AVCADVIRRW VYP LTPEAN FTDSTTQSCT HSRHNIYRGP EVSLGHGSIL EENVLLGSGT VIGSNCFITN SVIGPGCHIG DNVVLDQTYL WQGV RVAAG AQIHQSLLCD NAEVKERVTL KPRSVLTSQV VVGPNITLPE GSVISLHPPD AEEDEDDGEF SDDSGADQEK DKVKM KGYN PAEVGAAGKG YLWKAAGMNM EEEEELQQNL WGLKINMEEE SESESEQSMD SEEPDSRGGS PQMDDIKVFQ NEVLGT LQR GKEENISCDN LVLEINSLKY AYNISLKEVM QVLSHVVLEF PLQQMDSPLD SSRYCALLLP LLKAWSPVFR NYIKRAA DH LEALAAIEDF FLEHEALGIS MAKVLMAFYQ LEILAEETIL SWFSQRDTTD KGQQLRKNQQ LQRFIQWLKE AEEESSED D

UniProtKB: Translation initiation factor eIF2B subunit epsilon

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Macromolecule #6: Non-structural protein NS-S

MacromoleculeName: Non-structural protein NS-S / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sandfly fever sicilian virus
Molecular weightTheoretical: 29.695385 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSQYMFDYP AINIDVRCHR LLSSVSYVAY NKFHTHDVST YEHCEIPLEK LRLGFGRRNS LADFYSLGEL PASWGPACYF SSVKPMMYT FQGMASDLSR FDLTSFSRKG LPNVLKALSW PLGIPDCEIF SICSDRFVRG LQTRDQLMSY ILRMGDSHSL D ECIVQAHK ...String:
MNSQYMFDYP AINIDVRCHR LLSSVSYVAY NKFHTHDVST YEHCEIPLEK LRLGFGRRNS LADFYSLGEL PASWGPACYF SSVKPMMYT FQGMASDLSR FDLTSFSRKG LPNVLKALSW PLGIPDCEIF SICSDRFVRG LQTRDQLMSY ILRMGDSHSL D ECIVQAHK KILQEARRLG LSDEHYNGYD LFREIGSLVC LRLINAEPFD TASSGEALDV RTVIRSYRAS DPSTGLTEYG NS LWTPIHS HVDENDESSS DSDF

UniProtKB: Non-structural protein NS-S

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 888479
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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