2024-05-15 REL PDBe PDBe PDBe 2018-11-17 2019-05-22 2019-05-22 2024-05-15 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 Guaita M Adomavicius T Roseman AM Pavitt GD Translational control eIF2 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 EMD-4404 other EM volume
Same complex with phosphorylated serine
 6i7t 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 0.838 Translation initiation factor eIF-2B subunit alpha Saccharomyces cerevisiae 0.034062027 2 Saccharomyces cerevisiae LEVO MSEFNITETYLRFLEEDTEMTMPIAAIEALVTLLRIKTPETAAEMINTIKSSTEELIKSIPNSVSLRAGCDIFMRFVLRN LHLYGDWENCKQHLIENGQLFVSRAKKSRNKIAEIGVDFIADDDIILVHGYSRAVFSLLNHAANKFIRFRCVVTESRPSK QGNQLYTLLEQKGIPVTLIVDSAVGAVIDKVDKVFVGAEGVAESGGIINLVGTYSVGVLAHNARKPFYVVTESHKFVRMF PLSSDDLPMAGPPLDFTRRTDDLEDALRGPTIDYTAQEYITALITDLGVLTPSAVSEELIKMWYD P14741 Translation initiation factor eIF-2B subunit delta Saccharomyces cerevisiae 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 0.042621440999999996 2 Saccharomyces cerevisiae LEVO MSSQAFTSVHPNAATSDVNVTIDTFVAKLKRRQVQGSYAIALETLQLLMRFISAARWNHVNDLIEQIRDLGNSLEKAHPT AFSCGNVIRRILAVLRDEVEEDTMSTTVTSTSVAEPLISSMFNLLQKPEQPHQNRKNSSGSSSMKTKTDYRQVAIQGIKD LIDEIKNIDEGIQQIAIDLIHDHEILLTPTPDSKTVLKFLITARERSNRTFTVLVTEGFPNNTKNAHEFAKKLAQHNIET LVVPDSAVFALMSRVGKVIIGTKAVFVNGGTISSNSGVSSVCECAREFRTPVFAVAGLYKLSPLYPFDVEKFVEFGGSQR ILPRMDPRKRLDTVNQITDYVPPENIDIYITNVGGFNPSFIYRIAWDNYKQIDVHLDKNKA P32502 Translation initiation factor eIF-2B subunit epsilon Saccharomyces cerevisiae 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 0.06576832 2 Saccharomyces cerevisiae LEVO MSIQAFVFCGKGSNLAPFTQPDFPFQTQNKDSTAATSGDKLNELVNSALDSTVINEFMQHSTRLPKALLPIGNRPMIEYV LDWCDQADFKEISVVAPVDEIELIESGLTSFLSLRKQQFELIYKALSNSNHSHHLQDPKKINFIPSKANSTGESLQKELL PRINGDFVILPCDFVTDIPPQVLVDQFRNRDDNNLAMTIYYKNSLDSSIDKKQQQKQKQQQFFTVYSENEDSERQPILLD VYSQRDVTKTKYLQIRSHLLWNYPNLTVSTKLLNSFIYFCSFELCQLLKLGPQSMSRQASFKDPFTGNQQQQNPPTTDDD EDRNHDDDDDYKPSATSIQPTYFKKKNDLILDPINCNKSLSKVFRDLSRRSWQHSKPREPIGIFILPNETLFIRANNLNA YMDANRFVLKIKSQTMFTKNIQIQSAAIGADAIVDPKCQISAHSNVKMSVLGTQANIGSRCRVAGSLLFPGVHLGDEVIL ENCIIGPMAKIGSKCKLSNCYIEGHYVVEPKNNFKGETLANVYLDEDEEDELIYDDSVIAGESEIAEETDSDDRSDEDSD DSEYTDEYEYEDDGLFER P09032 Eukaryotic translation initiation factor 2 subunit alpha Saccharomyces cerevisiae 0.034763652 2 Saccharomyces cerevisiae LEVO MSTSHCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEK GYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDETVWEGIEP PSKDVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMSTEQMQVKVKLVAAPLYVLTTQALDKQKG IEQLESAIEKITEVITKYGGVCNITMPPKAVTATEDAELQALLESKELDNRSDSEDDEDESDDE P20459 Eukaryotic translation initiation factor 2 subunit beta Saccharomyces cerevisiae 0.031631308999999996 2 Saccharomyces cerevisiae LEVO MSSDLAAELGFDPALKKKKKTKKVIPDDFDAAVNGKENGSGDDLFAGLKKKKKKSKSVSADAEAEKEPTDDIAEALGELS LKKKKKKTKDSSVDAFEKELAKAGLDNVDAESKEGTPSANSSIQQEVGLPYSELLSRFFNILRTNNPELAGDRSGPKFRI PPPVCLRDGKKTIFSNIQDIAEKLHRSPEHLIQYLFAELGTSGSVDGQKRLVIKGKFQSKQMENVLRRYILEYVTCKTCK SINTELKREQSNRLFFMVCKSCGSTRSVSSIKTGFQATVGKRRRM P09064 Eukaryotic translation initiation factor 2 subunit gamma Saccharomyces cerevisiae 0.057942699 2 Saccharomyces cerevisiae LEVO MSDLQDQEPSIIINGNLEPVGEPDIVEETEVVAQETQETQDADKPKKKVAFTGLEEDGETEEEKRKREFEEGGGLPEQPL NPDFSKLNPLSAEIINRQATINIGTIGHVAHGKSTVVRAISGVQTVRFKDELERNITIKLGYANAKIYKCQEPTCPEPDC YRSFKSDKEISPKCQRPGCPGRYKLVRHVSFVDCPGHDILMSTMLSGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMK LKHVIILQNKVDLMREESALEHQKSILKFIRGTIADGAPIVPISAQLKYNIDAVNEFIVKTIPVPPRDFMISPRLIVIRS FDVNKPGAEIEDLKGGVAGGSILNGVFKLGDEIEIRPGIVTKDDKGKIQCKPIFSNIVSLFAEQNDLKFAVPGGLIGVGT KVDPTLCRADRLVGQVVGAKGHLPNIYTDIEINYFLLRRLLGVKTDGQKQAKVRKLEPNEVLMVNIGSTATGARVVAVKA DMARLQLTSPACTEINEKIALSRRIEKHWRLIGWATIKKGTTLEPIA P32481 singleParticle particle 0.28 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 ETHANE 100 294 FEI VITROBOT MARK III
Blot for 1 second before plunging.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 0.261 3.0 4.601 37313.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20
Tilt at 35 degrees.
GATAN K2 QUANTUM (4k x 4k) COUNTING 3838 3710 2-100 1 2154 10.0 1.0
Images were taken with 40, 60 or 100 frames in total. The first 2 frames were discarded in motioncorr2. The stage was tilted by 35 degrees.
 1 114390
2024 images were selected for particle picking. Initially, 3090 particles were picked manually and used for 2D classification into 20 classes. The best 8 classes (containing 2162 particles) were selected and used as references for automated particle picking in RELION. Particles on the lacey carbon, not in holes, were manually deleted in RELION, before extraction and further iterative cleaning by classification.
CryoEM map from RELION ab-initio model program
 C2 4.61 FSC 0.143 CUT-OFF RELION 2.1 23274 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 1 RELION 2.1 emd_4428.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 -0.061285395 0.15131684 0.0004001105 0.0060831057 1.34 1.34 1.34 0.045 AUTHOR eIF2B:eIF2 complex 6I3M A PDB experimental model 6I3M B PDB experimental model 6I3M C PDB experimental model 6I3M D PDB experimental model 6I3M E PDB experimental model 6I3M F PDB experimental model 6I3M G PDB experimental model 6I3M H PDB experimental model 6I3M I PDB experimental model 6I3M J PDB experimental model 6I3M K 3-174 PDB experimental model 6I3M L 3-174 PDB experimental model FLEXIBLE FIT
Our model of eIF2aP:eIF2B (PDB code:6I3M) was fitted and then iteratively 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, Fourier filtered 15A resolution, using UCSF_Chimera.
Cross-correlation coefficient REAL emd_4428_msk_1.map emd_4428_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 -0.15383944 0.42387587 0.0012292996 0.013261172 1.34 1.34 1.34 AUTHOR LocScale version of main map emd_4428_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 -0.02001797 0.056500323 0.00019954849 0.0027003903 1.34 1.34 1.34 AUTHOR Relion half-map 2 emd_4428_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 -0.020723283 0.058683187 0.00020063267 0.0027236785 1.34 1.34 1.34 AUTHOR Relion half-map 1