+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22924 | |||||||||
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Title | Sugar phosphate activation of the stress sensor eIF2B | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / guanyl-nucleotide exchange factor complex / oligodendrocyte development / 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 / guanyl-nucleotide exchange factor complex / oligodendrocyte development / astrocyte development / astrocyte differentiation / regulation of translational initiation / positive regulation of translational initiation / response to glucose / ovarian follicle development / translation initiation factor binding / response to endoplasmic reticulum stress / myelination / translation initiation factor activity / guanyl-nucleotide exchange factor activity / central nervous system development / hippocampus development / translational initiation / response to peptide hormone / regulation of translation / T cell receptor signaling pathway / response to heat / positive regulation of apoptotic process / GTP binding / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
Authors | Nocek B / Hao Q / Wong Y / Stoll V / Sidrauski C | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Sugar phosphate activation of the stress sensor eIF2B. Authors: Qi Hao / Jin-Mi Heo / Boguslaw P Nocek / Kevin G Hicks / Vincent S Stoll / Clint Remarcik / Sean Hackett / Lauren LeBon / Rinku Jain / Dan Eaton / Jared Rutter / Yao Liang Wong / Carmela Sidrauski / Abstract: The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. ...The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. The eIF2B regulatory subcomplex is evolutionarily related to sugar-metabolizing enzymes, but the biological relevance of this relationship was unknown. To identify natural ligands that might regulate eIF2B, we conduct unbiased binding- and activity-based screens followed by structural studies. We find that sugar phosphates occupy the ancestral catalytic site in the eIF2Bα subunit, promote eIF2B holoenzyme formation and enhance enzymatic activity towards eIF2. A mutant in the eIF2Bα ligand pocket that causes Vanishing White Matter disease fails to engage and is not stimulated by sugar phosphates. These data underscore the importance of allosteric metabolite modulation for proper eIF2B function. We propose that eIF2B evolved to couple nutrient status via sugar phosphate sensing with the rate of protein synthesis, one of the most energetically costly cellular processes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22924.map.gz | 141.6 MB | EMDB map data format | |
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Header (meta data) | emd-22924-v30.xml emd-22924.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
Images | emd_22924.png | 121.9 KB | ||
Others | emd_22924_half_map_1.map.gz emd_22924_half_map_2.map.gz | 139.1 MB 54.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22924 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22924 | HTTPS FTP |
-Validation report
Summary document | emd_22924_validation.pdf.gz | 809.1 KB | Display | EMDB validaton report |
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Full document | emd_22924_full_validation.pdf.gz | 808.7 KB | Display | |
Data in XML | emd_22924_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_22924_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22924 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22924 | HTTPS FTP |
-Related structure data
Related structure data | 7kmfMC 7kmaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22924.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_22924_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_22924_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tranlation initiation factor eif-2B
Entire | Name: Tranlation initiation factor eif-2B |
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Components |
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-Supramolecule #1: Tranlation initiation factor eif-2B
Supramolecule | Name: Tranlation initiation factor eif-2B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #5-#6 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Translation initiation factor eIF-2B subunit beta
Macromolecule | Name: Translation initiation factor eIF-2B subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.049633 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDYKDDDDKE NLYFQSMPGS AAKGSELSER IESFVETLKR GGGPRSSEEM ARETLGLLRQ IITDHRWSNA GELMELIRRE GRRMTAAQP SETTVGNMVR RVLKIIREEY GRLHGRSDES DQQESLHKLL TSGGLNEDFS FHYAQLQSNI IEAINELLVE L EGTMENIA ...String: MDYKDDDDKE NLYFQSMPGS AAKGSELSER IESFVETLKR GGGPRSSEEM ARETLGLLRQ IITDHRWSNA GELMELIRRE GRRMTAAQP SETTVGNMVR RVLKIIREEY GRLHGRSDES DQQESLHKLL TSGGLNEDFS FHYAQLQSNI IEAINELLVE L EGTMENIA AQALEHIHSN EVIMTIGFSR TVEAFLKEAA RKRKFHVIVA ECAPFCQGHE MAVNLSKAGI ETTVMTDAAI FA VMSRVNK VIIGTKTILA NGALRAVTGT HTLALAAKHH STPLIVCAPM FKLSPQFPNE EDSFHKFVAP EEVLPFTEGD ILE KVSVHC PVFDYVPPEL ITLFISNIGG NAPSYIYRLM SELYHPDDHV L |
-Macromolecule #2: Translation initiation factor eIF-2B subunit delta
Macromolecule | Name: Translation initiation factor eIF-2B subunit delta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.640168 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #3: Translation initiation factor eIF-2B subunit alpha
Macromolecule | Name: Translation initiation factor eIF-2B subunit alpha / type: protein_or_peptide / ID: 3 / Details: F6P / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.552938 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDDKELIEYF KSQMKEDPDM ASAVAAIRTL LEFLKRDKGE TIQGLRANLT SAIETLCGVD SSVAVSSGGE LFLRFISLAS LEYSDYSKC KKIMIERGEL FLRRISLSRN KIADLCHTFI KDGATILTHA YSRVVLRVLE AAVAAKKRFS VYVTESQPDL S GKKMAKAL ...String: MDDKELIEYF KSQMKEDPDM ASAVAAIRTL LEFLKRDKGE TIQGLRANLT SAIETLCGVD SSVAVSSGGE LFLRFISLAS LEYSDYSKC KKIMIERGEL FLRRISLSRN KIADLCHTFI KDGATILTHA YSRVVLRVLE AAVAAKKRFS VYVTESQPDL S GKKMAKAL CHLNVPVTVV LDAAVGYIME KADLVIVGAE GVVENGGIIN KIGTNQMAVC AKAQNKPFYV VAESFKFVRL FP LNQQDVP DKFKYKADTL KVAQTGQDLK EEHPWVDYTA PSLITLLFTD LGVLTPSAVS DELIKLYLGG ENLYFQAEDK GGG SGGGGS GGGGSASQGG LNDIFEAQKI EWHEGGGGSG GGGSGGGGSG RDQDYKDDDD K |
-Macromolecule #4: Translation initiation factor eIF-2B subunit epsilon
Macromolecule | Name: Translation initiation factor eIF-2B subunit epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 80.466609 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #5: Translation initiation factor eIF-2B subunit gamma
Macromolecule | Name: Translation initiation factor eIF-2B subunit gamma / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.30423 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #6: 6-O-phosphono-beta-D-fructofuranose
Macromolecule | Name: 6-O-phosphono-beta-D-fructofuranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: F6P |
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Molecular weight | Theoretical: 260.136 Da |
Chemical component information | ChemComp-F6P: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 18 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.32 mg/mL |
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Buffer | pH: 7.5 Details: Prior to grid preparation, the protein mixture was diluted with 25 mM HEPES, 100 mM KCl, 2 mM 446 MgCl2, 1 mM DTT, pH 7.5 to |
Vitrification | Cryogen name: ETHANE |
Details | eif2a was mixed with eif2bcde in 1.5 :1 molar ratio and incubated on ice. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6073 / Average electron dose: 44.33 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 73704 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |