2024-11-06 REL PDBe PDBe PDBe 2018-11-06 2019-05-08 2019-05-22 2024-11-06 Biotechnology and Biological Sciences Research Council BB/L020157/1 United Kingdom Biotechnology and Biological Sciences Research Council BB/N014049/1 United Kingdom Biotechnology and Biological Sciences Research Council BB/M006565/1 United Kingdom Biotechnology and Biological Sciences Research Council BB/M011208/1 United Kingdom eIF2B:eIF2 complex, phosphorylated on eIF2 alpha serine 52. Adomavicius T Roseman AM Translational control eIF2 phosphorylation Integrated stress response eIF2B TRANSLATION, TRANSLATION Adomavicius T Guaita M Zhou Y Jennings MD Latif Z Roseman AM Pavitt GD The structural basis of translational control by eIF2 phosphorylation. Nat Commun UK 10 2136 2136 2019 31086188 doi:10.1038/s41467-019-10167-3 2041-1723 Jennings MD Kershaw CJ Adomavicius T Pavitt GD Fail-safe control of translation initiation by dissociation of eIF2 alpha phosphorylated ternary complexes. Elife US 6 2017 28315520 doi:10.7554/eLife.24542 2050-084X 6i3m FULLOVERLAP Complex of translation initiation factors eIF2 and eIF2B Complex of translation initiation factors eIF2 and eIF2B 0 1 2 3 4 5 6 7 8 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.838 Translation initiation factor eIF-2B subunit alpha Saccharomyces cerevisiae S288C 0.034062027 2 Saccharomyces cerevisiae LEVO MSEFNITETYLRFLEEDTEMTMPIAAIEALVTLLRIKTPETAAEMINTIKSSTEELIKSIPNSVSLRAGCDIFMRFVLRN LHLYGDWENCKQHLIENGQLFVSRAKKSRNKIAEIGVDFIADDDIILVHGYSRAVFSLLNHAANKFIRFRCVVTESRPSK QGNQLYTLLEQKGIPVTLIVDSAVGAVIDKVDKVFVGAEGVAESGGIINLVGTYSVGVLAHNARKPFYVVTESHKFVRMF PLSSDDLPMAGPPLDFTRRTDDLEDALRGPTIDYTAQEYITALITDLGVLTPSAVSEELIKMWYD P14741 Translation initiation factor eIF-2B subunit delta Saccharomyces cerevisiae S288C 0.070945195 2 Saccharomyces cerevisiae LEVO MSESEAKSRSATPPSKAKQATPTTTAAANGEKKLTNKELKELKKQEKAAKRAAMKQANGISIEQQQQQAQMKKEKKQLQR EQQQKREQKQKNANKKKQNERNVKKSTLFGHLETTEERRATILALTSAVSSPKTSRITAAGLMVPVVASALSGSNVLTAS SLMPVGPNASSTVSASAPASTTTTLPASSAALSAGTSSASTNTPTAIQQEIASSNASDVAKTLASISLEAGEFNVIPGIS SVIPTVLEQSFDNSSLISSVKELLLNKDLIHPSILLLTSHLAHYKIVGSIPRCIAMLEVFQIVIKDYQTPKGTTLSRNLT SYLSHQIDLLKKARPLSVTMGNAIRWLKQEISLIDPSTPDKAAKKDLCEKIGQFAKEKIELADQLIIDNASTQIEESTTI VTYGSSKVLTELLLHNAISLKKNIKVIVVDSRPLFEGRKMAETLRNAGVNVMYALITSLDTIFNMDVDYVFLGAHSILSN GFLYSRAGTAMLAMSAKRRNIPVLVCCESLKFSQRVQLDSVTFNELADPNDLVNIDYENPVERRGNKGALLNQFIKERKF EKKKLAMENKPKGNKIGGKKGSEGESKDASNEEDSNSKNILDGWQELPSLNIVNILYDLTPPEYIKKVITEFGALPPSSV PVILREYKGSA P12754 Translation initiation factor eIF-2B subunit beta Saccharomyces cerevisiae S288C 0.042621440999999996 2 Saccharomyces cerevisiae LEVO MSSQAFTSVHPNAATSDVNVTIDTFVAKLKRRQVQGSYAIALETLQLLMRFISAARWNHVNDLIEQIRDLGNSLEKAHPT AFSCGNVIRRILAVLRDEVEEDTMSTTVTSTSVAEPLISSMFNLLQKPEQPHQNRKNSSGSSSMKTKTDYRQVAIQGIKD LIDEIKNIDEGIQQIAIDLIHDHEILLTPTPDSKTVLKFLITARERSNRTFTVLVTEGFPNNTKNAHEFAKKLAQHNIET LVVPDSAVFALMSRVGKVIIGTKAVFVNGGTISSNSGVSSVCECAREFRTPVFAVAGLYKLSPLYPFDVEKFVEFGGSQR ILPRMDPRKRLDTVNQITDYVPPENIDIYITNVGGFNPSFIYRIAWDNYKQIDVHLDKNKA P32502 Translation initiation factor eIF-2B subunit epsilon Saccharomyces cerevisiae S288C 0.081249062 2 Saccharomyces cerevisiae LEVO MAGKKGQKKSGLGNHGKNSDMDVEDRLQAVVLTDSYETRFMPLTAVKPRCLLPLANVPLIEYTLEFLAKAGVHEVFLICS SHANQINDYIENSKWNLPWSPFKITTIMSPEARCTGDVMRDLDNRGIITGDFILVSGDVLTNIDFSKMLEFHKKMHLQDK DHISTMCLSKASTYPKTRTIEPAAFVLDKSTSRCIYYQDLPLPSSREKTSIQIDPELLDNVDEFVIRNDLIDCRIDICTS HVPLIFQENFDYQSLRTDFVKGVISSDILGKHIYAYLTDEYAVRVESWQTYDTISQDFLGRWCYPLVLDSNIQDDQTYSY ESRHIYKEKDVVLAQSCKIGKCTAIGSGTKIGEGTKIENSVIGRNCQIGENIRIKNSFIWDDCIIGNNSIIDHSLIASNA TLGSNVRLNDGCIIGFNVKIDDNMDLDRNTKISASPLKNAGSRMYDNESNEQFDQDLDDQTLAVSIVGDKGVGYIYESEV SDDEDSSTEACKEINTLSNQLDELYLSDDSISSATKKTKKRRTMSVNSIYTDREEIDSEFEDEDFEKEGIATVERAMENN HDLDTALLELNTLRMSMNVTYHEVRIATITALLRRVYHFIATQTLGPKDAVVKVFNQWGLLFKRQAFDEEEYIDLMNIIM EKIVEQSFDKPDLILFSALVSLYDNDIIEEDVIYKWWDNVSTDPRYDEVKKLTVKWVEWLQNADEESSSEEE P32501 Translation initiation factor eIF-2B subunit gamma Saccharomyces cerevisiae S288C 0.06576832 2 Saccharomyces cerevisiae LEVO MSIQAFVFCGKGSNLAPFTQPDFPFQTQNKDSTAATSGDKLNELVNSALDSTVINEFMQHSTRLPKALLPIGNRPMIEYV LDWCDQADFKEISVVAPVDEIELIESGLTSFLSLRKQQFELIYKALSNSNHSHHLQDPKKINFIPSKANSTGESLQKELL PRINGDFVILPCDFVTDIPPQVLVDQFRNRDDNNLAMTIYYKNSLDSSIDKKQQQKQKQQQFFTVYSENEDSERQPILLD VYSQRDVTKTKYLQIRSHLLWNYPNLTVSTKLLNSFIYFCSFELCQLLKLGPQSMSRQASFKDPFTGNQQQQNPPTTDDD EDRNHDDDDDYKPSATSIQPTYFKKKNDLILDPINCNKSLSKVFRDLSRRSWQHSKPREPIGIFILPNETLFIRANNLNA YMDANRFVLKIKSQTMFTKNIQIQSAAIGADAIVDPKCQISAHSNVKMSVLGTQANIGSRCRVAGSLLFPGVHLGDEVIL ENCIIGPMAKIGSKCKLSNCYIEGHYVVEPKNNFKGETLANVYLDEDEEDELIYDDSVIAGESEIAEETDSDDRSDEDSD DSEYTDEYEYEDDGLFER P09032 Eukaryotic translation initiation factor 2 subunit alpha Saccharomyces cerevisiae S288C 0.034843633 2 Saccharomyces cerevisiae LEVO MSTSHCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSEL(SEP)RRRIRSIQKLIRVGKNDVAVVLRV DKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDETVWE GIEPPSKDVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMSTEQMQVKVKLVAAPLYVLTTQALD KQKGIEQLESAIEKITEVITKYGGVCNITMPPKAVTATEDAELQALLESKELDNRSDSEDDEDESDDE P20459 Eukaryotic translation initiation factor 2 subunit beta Saccharomyces cerevisiae S288C 0.031631308999999996 2 Saccharomyces cerevisiae LEVO MSSDLAAELGFDPALKKKKKTKKVIPDDFDAAVNGKENGSGDDLFAGLKKKKKKSKSVSADAEAEKEPTDDIAEALGELS LKKKKKKTKDSSVDAFEKELAKAGLDNVDAESKEGTPSANSSIQQEVGLPYSELLSRFFNILRTNNPELAGDRSGPKFRI PPPVCLRDGKKTIFSNIQDIAEKLHRSPEHLIQYLFAELGTSGSVDGQKRLVIKGKFQSKQMENVLRRYILEYVTCKTCK SINTELKREQSNRLFFMVCKSCGSTRSVSSIKTGFQATVGKRRRM P09064 Eukaryotic translation initiation factor 2 subunit gamma Saccharomyces cerevisiae S288C 0.057942699 2 Saccharomyces cerevisiae LEVO MSDLQDQEPSIIINGNLEPVGEPDIVEETEVVAQETQETQDADKPKKKVAFTGLEEDGETEEEKRKREFEEGGGLPEQPL NPDFSKLNPLSAEIINRQATINIGTIGHVAHGKSTVVRAISGVQTVRFKDELERNITIKLGYANAKIYKCQEPTCPEPDC YRSFKSDKEISPKCQRPGCPGRYKLVRHVSFVDCPGHDILMSTMLSGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMK LKHVIILQNKVDLMREESALEHQKSILKFIRGTIADGAPIVPISAQLKYNIDAVNEFIVKTIPVPPRDFMISPRLIVIRS FDVNKPGAEIEDLKGGVAGGSILNGVFKLGDEIEIRPGIVTKDDKGKIQCKPIFSNIVSLFAEQNDLKFAVPGGLIGVGT KVDPTLCRADRLVGQVVGAKGHLPNIYTDIEINYFLLRRLLGVKTDGQKQAKVRKLEPNEVLMVNIGSTATGARVVAVKA DMARLQLTSPACTEINEKIALSRRIEKHWRLIGWATIKKGTTLEPIA P32481 singleParticle particle 0.25 7.5 100.0 KCl potassium chloride 20.0 Tris 1.0 TCEP
Solutions for sample preparation were made fresh, filter sterilized, and degassed.
 Homemade COPPER 400 CARBON LACEY CARBON CONTINUOUS 3.0 GLOW DISCHARGE AIR 101.325
Ultra-thin carbon support film, 3nm - on lacey carbon grids from Agar Scientific were used for 35 degree tilted data collection. For zero tilt data collection, 200 mesh Au Quantifoil, R2/2 grids were used.
 ETHANE 100 294 FEI VITROBOT MARK III
Blot for 2 seconds before plunging.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.5 1.0 4.0 5.5 37313.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20
Tilt at zero and 35 degrees.
GATAN K2 QUANTUM (4k x 4k) COUNTING 3838 3710 2-48 2 4533 12.0 40.0
2 separate data collections for zero degree (2255 images) and tilted (2278 images) specimen. Both on Titan Krios
 1 655000
Initially, approximately 3000 particles were picked manually and used for 2D classification. Then 4 best looking 2D class average images were used as references for automated particle picking in RELION. For the zero tilt data collection, 406000 particles were picked. For the 35 degree tilt data collection, 249000 particles were picked
Initial model was generated in Cryosparc.
 C2 3.93 FSC 0.143 CUT-OFF RELION 2.1 64541 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 1 RELION 2.1 emd_4404.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 428.80002 428.80002 428.80002 90.0 90.0 90.0 X Y Z -0.18108554 0.3041722 0.00024270266 0.008404886 1.34 1.34 1.34 0.055 AUTHOR eIF2B:eIF2 complex with eIF2 alpha phosphorylated on serine 52 5B04 PDB experimental model 3JAP j 3-174 PDB experimental model FLEXIBLE FIT
Modeller was used to build homology model of S. cerevisiae eIF2B structure based on S. pombe crystal structure. Subunits of the homology model, along with eIF2 alpha domains 1 and 2, were then rigid body fitted into our map using UCSF Chimera. The model then was refined using phenix and manually adjusted in Coot.
correlation coeficient REAL 3JAP j 182-265 PDB experimental model 3JAP k PDB experimental model 3JAP l 127-143 PDB experimental model RIGID BODY FIT
eIF2 alpha domain 3, eIF2 gamma, and eIF2 beta (3JAP) were rigid body fitted into our map using Chimera.
Cross-correlation coefficient REAL emd_4404_msk_1.map emd_4404_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 428.80002 428.80002 428.80002 90.0 90.0 90.0 X Y Z -0.19225763 0.532957 0.0010794027 0.014409717 1.34 1.34 1.34 AUTHOR LocScale version of main map emd_4404_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 428.80002 428.80002 428.80002 90.0 90.0 90.0 X Y Z -0.024785442 0.06450002 0.000116145 0.0024568175 1.34 1.34 1.34 AUTHOR relion half-map 1 emd_4404_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 428.80002 428.80002 428.80002 90.0 90.0 90.0 X Y Z -0.024535805 0.0626251 0.00012655766 0.0024643743 1.34 1.34 1.34 AUTHOR relion half-map 2