Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (map 1)

2024-10-16 REL PDBe PDBe PDBe 2019-01-10 2016-08-24 2019-06-26 2024-10-16 Medical Research Council (United Kingdom) MC_U105184332 United Kingdom Wellcome Trust WT096570 United Kingdom Spanish Ministry of Economy and Competitiveness BFU2017-85814-P Spain Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (map 1) Llacer JL Gordiyenko Y Ramakrishnan V Ramakrishnan V integrated stress response, ISR, translation, initiation factors, phosphorylation, eIF2, eIF2B, tRNAi, GEF, heat domain, eIF2 alpha Gordiyenko Y Llacer JL Ramakrishnan V Structural basis for the inhibition of translation through eIF2 alpha phosphorylation. Nat Commun UK 10 2640 2640 2019 31201334 doi:10.1038/s41467-019-10606-1 2041-1723 6qg0 FULLOVERLAP Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 1) Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 1) 0 1 2 3 4 5 6 7 8 Saccharomyces cerevisiae S288C 0.837 Translation initiation factor eIF-2B subunit alpha Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.034062027 2 Saccharomyces cerevisiae LEVO MSEFNITETYLRFLEEDTEMTMPIAAIEALVTLLRIKTPETAAEMINTIKSSTEELIKSIPNSVSLRAGCDIFMRFVLRN LHLYGDWENCKQHLIENGQLFVSRAKKSRNKIAEIGVDFIADDDIILVHGYSRAVFSLLNHAANKFIRFRCVVTESRPSK QGNQLYTLLEQKGIPVTLIVDSAVGAVIDKVDKVFVGAEGVAESGGIINLVGTYSVGVLAHNARKPFYVVTESHKFVRMF PLSSDDLPMAGPPLDFTRRTDDLEDALRGPTIDYTAQEYITALITDLGVLTPSAVSEELIKMWYD P14741 Translation initiation factor eIF-2B subunit beta Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.042621440999999996 2 Saccharomyces cerevisiae LEVO MSSQAFTSVHPNAATSDVNVTIDTFVAKLKRRQVQGSYAIALETLQLLMRFISAARWNHVNDLIEQIRDLGNSLEKAHPT AFSCGNVIRRILAVLRDEVEEDTMSTTVTSTSVAEPLISSMFNLLQKPEQPHQNRKNSSGSSSMKTKTDYRQVAIQGIKD LIDEIKNIDEGIQQIAIDLIHDHEILLTPTPDSKTVLKFLITARERSNRTFTVLVTEGFPNNTKNAHEFAKKLAQHNIET LVVPDSAVFALMSRVGKVIIGTKAVFVNGGTISSNSGVSSVCECAREFRTPVFAVAGLYKLSPLYPFDVEKFVEFGGSQR ILPRMDPRKRLDTVNQITDYVPPENIDIYITNVGGFNPSFIYRIAWDNYKQIDVHLDKNKA P32502 Translation initiation factor eIF-2B subunit gamma Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.06576832 2 Saccharomyces cerevisiae LEVO MSIQAFVFCGKGSNLAPFTQPDFPFQTQNKDSTAATSGDKLNELVNSALDSTVINEFMQHSTRLPKALLPIGNRPMIEYV LDWCDQADFKEISVVAPVDEIELIESGLTSFLSLRKQQFELIYKALSNSNHSHHLQDPKKINFIPSKANSTGESLQKELL PRINGDFVILPCDFVTDIPPQVLVDQFRNRDDNNLAMTIYYKNSLDSSIDKKQQQKQKQQQFFTVYSENEDSERQPILLD VYSQRDVTKTKYLQIRSHLLWNYPNLTVSTKLLNSFIYFCSFELCQLLKLGPQSMSRQASFKDPFTGNQQQQNPPTTDDD EDRNHDDDDDYKPSATSIQPTYFKKKNDLILDPINCNKSLSKVFRDLSRRSWQHSKPREPIGIFILPNETLFIRANNLNA YMDANRFVLKIKSQTMFTKNIQIQSAAIGADAIVDPKCQISAHSNVKMSVLGTQANIGSRCRVAGSLLFPGVHLGDEVIL ENCIIGPMAKIGSKCKLSNCYIEGHYVVEPKNNFKGETLANVYLDEDEEDELIYDDSVIAGESEIAEETDSDDRSDEDSD DSEYTDEYEYEDDGLFER P09032 Translation initiation factor eIF-2B subunit delta Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.070945195 2 Saccharomyces cerevisiae LEVO MSESEAKSRSATPPSKAKQATPTTTAAANGEKKLTNKELKELKKQEKAAKRAAMKQANGISIEQQQQQAQMKKEKKQLQR EQQQKREQKQKNANKKKQNERNVKKSTLFGHLETTEERRATILALTSAVSSPKTSRITAAGLMVPVVASALSGSNVLTAS SLMPVGPNASSTVSASAPASTTTTLPASSAALSAGTSSASTNTPTAIQQEIASSNASDVAKTLASISLEAGEFNVIPGIS SVIPTVLEQSFDNSSLISSVKELLLNKDLIHPSILLLTSHLAHYKIVGSIPRCIAMLEVFQIVIKDYQTPKGTTLSRNLT SYLSHQIDLLKKARPLSVTMGNAIRWLKQEISLIDPSTPDKAAKKDLCEKIGQFAKEKIELADQLIIDNASTQIEESTTI VTYGSSKVLTELLLHNAISLKKNIKVIVVDSRPLFEGRKMAETLRNAGVNVMYALITSLDTIFNMDVDYVFLGAHSILSN GFLYSRAGTAMLAMSAKRRNIPVLVCCESLKFSQRVQLDSVTFNELADPNDLVNIDYENPVERRGNKGALLNQFIKERKF EKKKLAMENKPKGNKIGGKKGSEGESKDASNEEDSNSKNILDGWQELPSLNIVNILYDLTPPEYIKKVITEFGALPPSSV PVILREYKGSA P12754 Translation initiation factor eIF-2B subunit epsilon Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.081249062 2 Saccharomyces cerevisiae LEVO MAGKKGQKKSGLGNHGKNSDMDVEDRLQAVVLTDSYETRFMPLTAVKPRCLLPLANVPLIEYTLEFLAKAGVHEVFLICS SHANQINDYIENSKWNLPWSPFKITTIMSPEARCTGDVMRDLDNRGIITGDFILVSGDVLTNIDFSKMLEFHKKMHLQDK DHISTMCLSKASTYPKTRTIEPAAFVLDKSTSRCIYYQDLPLPSSREKTSIQIDPELLDNVDEFVIRNDLIDCRIDICTS HVPLIFQENFDYQSLRTDFVKGVISSDILGKHIYAYLTDEYAVRVESWQTYDTISQDFLGRWCYPLVLDSNIQDDQTYSY ESRHIYKEKDVVLAQSCKIGKCTAIGSGTKIGEGTKIENSVIGRNCQIGENIRIKNSFIWDDCIIGNNSIIDHSLIASNA TLGSNVRLNDGCIIGFNVKIDDNMDLDRNTKISASPLKNAGSRMYDNESNEQFDQDLDDQTLAVSIVGDKGVGYIYESEV SDDEDSSTEACKEINTLSNQLDELYLSDDSISSATKKTKKRRTMSVNSIYTDREEIDSEFEDEDFEKEGIATVERAMENN HDLDTALLELNTLRMSMNVTYHEVRIATITALLRRVYHFIATQTLGPKDAVVKVFNQWGLLFKRQAFDEEEYIDLMNIIM EKIVEQSFDKPDLILFSALVSLYDNDIIEEDVIYKWWDNVSTDPRYDEVKKLTVKWVEWLQNADEESSSEEE P32501 Eukaryotic translation initiation factor 2 subunit alpha Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.034843633 2 Saccharomyces cerevisiae LEVO MSTSHCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSEL(SEP)RRRIRSIQKLIRVGKNDVAVVLRV DKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDETVWE GIEPPSKDVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMSTEQMQVKVKLVAAPLYVLTTQALD KQKGIEQLESAIEKITEVITKYGGVCNITMPPKAVTATEDAELQALLESKELDNRSDSEDDEDESDDE P20459 Eukaryotic translation initiation factor 2 subunit gamma Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.057942699 2 Saccharomyces cerevisiae LEVO MSDLQDQEPSIIINGNLEPVGEPDIVEETEVVAQETQETQDADKPKKKVAFTGLEEDGETEEEKRKREFEEGGGLPEQPL NPDFSKLNPLSAEIINRQATINIGTIGHVAHGKSTVVRAISGVQTVRFKDELERNITIKLGYANAKIYKCQEPTCPEPDC YRSFKSDKEISPKCQRPGCPGRYKLVRHVSFVDCPGHDILMSTMLSGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMK LKHVIILQNKVDLMREESALEHQKSILKFIRGTIADGAPIVPISAQLKYNIDAVNEFIVKTIPVPPRDFMISPRLIVIRS FDVNKPGAEIEDLKGGVAGGSILNGVFKLGDEIEIRPGIVTKDDKGKIQCKPIFSNIVSLFAEQNDLKFAVPGGLIGVGT KVDPTLCRADRLVGQVVGAKGHLPNIYTDIEINYFLLRRLLGVKTDGQKQAKVRKLEPNEVLMVNIGSTATGARVVAVKA DMARLQLTSPACTEINEKIALSRRIEKHWRLIGWATIKKGTTLEPIA P32481 Eukaryotic translation initiation factor 2 subunit beta Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.031631308999999996 2 Saccharomyces cerevisiae LEVO MSSDLAAELGFDPALKKKKKTKKVIPDDFDAAVNGKENGSGDDLFAGLKKKKKKSKSVSADAEAEKEPTDDIAEALGELS LKKKKKKTKDSSVDAFEKELAKAGLDNVDAESKEGTPSANSSIQQEVGLPYSELLSRFFNILRTNNPELAGDRSGPKFRI PPPVCLRDGKKTIFSNIQDIAEKLHRSPEHLIQYLFAELGTSGSVDGQKRLVIKGKFQSKQMENVLRRYILEYVTCKTCK SINTELKREQSNRLFFMVCKSCGSTRSVSSIKTGFQATVGKRRRM P09064 singleParticle particle 0.17 7.5 20.0 Hepes 5.0 Magnessium chloride 100.0 Potassium chloride 5.0 beta mercaptoethanol Quantifoil, UltrAuFoil GOLD 300 GLOW DISCHARGE 15 ETHANE 100 277 FEI VITROBOT MARK I FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.5 3.5 59000.0 104478.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 90.0 100.0 FEI FALCON III (4k x 4k) COUNTING 2 1241 60.0 21.0

Images were collected in movie-mode at 32 frames per second

FEI Falcon III

173740 5B04

Low pass filtered to 60 angstrom

C2 4.15 FSC 0.143 CUT-OFF RELION 2 131663 NOT APPLICABLE RELION 2 MAXIMUM LIKELIHOOD RELION 2 RELION 2 emd_4543.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 375.2 375.2 375.2 90.0 90.0 90.0 X Y Z -0.3406921 0.57914305 -0.00004687786 0.012737702 1.34 1.34 1.34 0.06 AUTHOR ::::EMDATABANK.org::::EMD-4543:::: For optimal visualization of all eIF2 alpha and gamma, gauss-filter the map by 1.34 and display it at 0.022 contour level OTHER FSC RECIPROCAL emd_4543_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 375.2 375.2 375.2 90.0 90.0 90.0 X Y Z -0.026713014 0.065905035 -0.00002320398 0.0025465202 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::EMD-4543:::: emd_4543_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 375.2 375.2 375.2 90.0 90.0 90.0 X Y Z -0.026215876 0.06503928 -0.00002367388 0.002540961 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::EMD-4543::::