2024-05-15 REL PDBe PDBe PDBe 2019-01-28 2019-02-06 2019-07-17 2024-05-15 German Research Foundation BR921/9-1 & Mu3173/2-1 Germany Polish National Science Centre UMO-2015/19/B/NZ1/00343 Poland Elongator catalytic subcomplex Elp123 lobe Dauden MI Weis F Elongator, yeast, tRNA modification, Elp123, TRANSLATION Dauden MI Jaciuk M Weis F Lin TY Kleindienst C Abbassi NEH Khatter H Krutyholowa R Breunig KD Kosinski J Muller CW Glatt S Molecular basis of tRNA recognition by the Elongator complex. Sci Adv US 5 eaaw2326 eaaw2326 2019 31309145 doi:10.1126/sciadv.aaw2326 2375-2548 6qk7 FULLOVERLAP Elongator catalytic subcomplex Elp123 Elongator catalytic subcomplex Elp123 0 1 2 3
The EM map corresponds to one lobe of the Elp123 complex, that includes one copy of Elp1, Elp2 and Elp3, and the C-terminal part of a second copy of Elp1.
Saccharomyces cerevisiae 0.621 Elongator complex protein 1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.153166266
Chain D corresponds to the C-terminal domain of Elp1
2 LEVO MVEHDKSGSKRQELRSNMRNLITLNKGKFKPTASTAEGDEDDLSFTLLDSVFDTLSDSITCVLGSTDIGAIEVQQFMKDG SRNVLASFNIQTFDDKLLSFVHFADINQLVFVFEQGDIITATYDPVSLDPAETLIEIMGTIDNGIAAAQWSYDEETLAMV TKDRNVVVLSKLFEPISEYHLEVDDLKISKHVTVGWGKKETQFRGKGARAMEREALASLKASGLVGNQLRDPTMPYMVDT GDVTALDSHEITISWRGDCDYFAVSSVEEVPDEDDETKSIKRRAFRVFSREGQLDSASEPVTGMEHQLSWKPQGSLIASI QRKTDLGEEDSVDVIFFERNGLRHGEFDTRLPLDEKVESVCWNSNSEALAVVLANRIQLWTSKNYHWYLKQELYASDISY VKWHPEKDFTLMFSDAGFINIVDFAYKMAQGPTLEPFDNGTSLVVDGRTVNITPLALANVPPPMYYRDFETPGNVLDVAC SFSNEIYAAINKDVLIFAAVPSIEEMKKGKHPSIVCEFPKSEFTSEVDSLRQVAFINDSIVGVLLDTDNLSRIALLDIQD ITQPTLITIVEVYDKIVLLRSDFDYNHLVYETRDGTVCQLDAEGQLMEITKFPQLVRDFRVKRVHNTSAEDDDNWSAESS ELVAFGITNNGKLFANQVLLASAVTSLEITDSFLLFTTAQHNLQFVHLNSTDFKPLPLVEEGVEDERVRAIERGSILVSV IPSKSSVVLQATRGNLETIYPRIMVLAEVRKNIMAKRYKEAFIVCRTHRINLDILHDYAPELFIENLEVFINQIGRVDYL NLFISCLSEDDVTKTKYKETLYSGISKSFGMEPAPLTEMQIYMKKKMFDPKTSKVNKICDAVLNVLLSNPEYKKKYLQTI ITAYASQNPQNLSAALKLISELENSEEKDSCVTYLCFLQDVNVVYKSALSLYDVSLALLVAQKSQMDPREYLPFLQELQD NEPLRRKFLIDDYLGNYEKALEHLSEIDKDGNVSEEVIDYVESHDLYKHGLALYRYDSEKQNVIYNIYAKHLSSNQMYTD AAVAYEMLGKLKEAMGAYQSAKRWREAMSIAVQKFPEEVESVAEELISSLTFEHRYVDAADIQLEYLDNVKEAVALYCKA YRYDIASLVAIKAKKDELLEEVVDPGLGEGFGIIAELLADCKGQINSQLRRLRELRAKKEENPYAFYGQETEQADDVSVA PSETSTQESFFTRYTGKTGGTAKTGASRRTAKNKRREERKRARGKKGTIYEEEYLVQSVGRLIERLNQTKPDAVRVVEGL CRRNMREQAHQIQKNFVEVLDLLKANVKEIYSISEKDRERVNENGEVYYIPEIPVPEIHDFPKSHIVDF Q06706 Elongator complex protein 2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.08951942999999998 1 LEVO MVECITPEAIFIGANKQTQVSDIHKVKKIVAFGAGKTIALWDPIEPNNKGVYATLKGHEAEVTCVRFVPDSDFMVSASED HHVKIWKFTDYSHLQCIQTIQHYSKTIVALSALPSLISVGCADGTISIWRQNIQNDEFGLAHEFTIKKGFFYPLCLSLSK VEEKKYLLAIGGTNVNVFIASFILSDSGIEKCRVVAELEGHEDWVKSLAFRHQETPGDYLLCSGSQDRYIRLWRIRINDL IDDSEEDSKKLTLLSNKQYKFQIDDELRVGINFEALIMGHDDWISSLQWHESRLQLLAATADTSLMVWEPDETSGIWVCS LRLGEMSSKGASTATGSSGGFWSCLWFTHERMDFFLTNGKTGSWRMWATKDNIICDQRLGISGATKDVTDIAWSPSGEYL LATSLDQTTRLFAPWIYDASGRKREIATWHEFSRPQIHGYDMICVETVTDTRFVSGGDEKILRSFDLPKGVAGMLQKFVG IQFEEKSEMPDSATVPVLGLSNKAGEDDANEDDEEEEGGNKETPDITDPLSLLECPPMEDQLQRHLLWPEVEKLYGHGFE ITCLDISPDQKLIASACRSNNVQNAVIRIFSTENWLEIKPALPFHSLTITRLKFSKDGKFLLSVCRDRKWALWERNMEDN TFELRFKNEKPHTRIIWDADWAPLEFGNVFVTASRDKTVKVWRHQKEPADDYVLEASIKHTKAVTAISIHDSMIREKILI SVGLENGEIYLYSYTLGKFELITQLNEDITPADKITRLRWSHLKRNGKLFLGVGSSDLSTRIYSLAYE P42935 Elongator complex protein 3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.063755059
FeS cluster and 5DA
1 LEVO MARHGKGPKTNKKKLAPEKERFIQCCADITLELTDSLTSGTTREINLNGLITKYSKKYKLKQQPRLTDIINSIPDQYKKY LLPKLKAKPVRTASGIAVVAVMCKPHRCPHIAYTGNICVYCPGGPDSDFEYSTQSYTGYEPTSMRAIRARYDPYEQARGR VEQLKQLGHSIDKVEYVLMGGTFMSLPKEYREDFIVKLHNALSGFNGNDIDEAILYSQQSLTKCVGITIETRPDYCTQTH LDDMLKYGCTRLEIGVQSLYEDVARDTNRGHTVRSVCETFAVSKDAGYKVVSHMMPDLPNVGMERDIEQFKEYFENPDFR TDGLKIYPTLVIRGTGLYELWKTGRYKSYSANALVDLVARILALVPPWTRIYRVQRDIPMPLVTSGVDNGNLRELALARM KDLGTTCRDVRTREVGIQEVHHKVQPDQVELIRRDYYANGGWETFLSYEDPKKDILIGLLRLRKASKKYTYRKEFTSQRT SIVRELHVYGSVVPLHSRDPRKFQHQGFGTLLMEEAERIAKEEHGSEKISVISGVGVRNYYGKLGYELDGPYMSKRI Q02908 2.3.1.48 IRON/SULFUR CLUSTER 0.00035163999999999996 1 SF4 5'-DEOXYADENOSINE 0.000251242 1 5AD singleParticle particle 0.4 7.5 10.0 Hepes Hepes 125.0 NaCl Sodium chloride 50.0 NaF Sodium fluoride 0.1 Na3VO4 Sodium vanadate 5.0 C2H6OS beta-mercaptoethanol Quantifoil R2/1 COPPER 200 GLOW DISCHARGE
Pelco EasyGlow glow discharger, 20 mA
 ETHANE 100 277 FEI VITROBOT MARK IV
2.5 ul of sample, blotting parameters: wait time 15 s, blot force 5, blot time 5-8 s..
The sample was cross-linked with 0.01% glutaraldehyde, quenched and then plunged.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 105000.0
Gatan Quantum energy filter and a K2 Summit direct detector
GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 4614 43.0 1
The detector was operated in super resolution mode.
1000000
Initially 8563 particles were manually selected using EMAN2 boxer swarm tool, and used as 2D templates for the autopicking procedure in relion, that yielded 1 million particles.
 EMD-4151
The initial model was low pass filtered to 60 A.
 2 C1 3.3 FSC 0.143 CUT-OFF RELION 2 84135 MAXIMUM LIKELIHOOD RELION 2 MAXIMUM LIKELIHOOD RELION 2 4 39000.0 emd_4571.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 290 290 290 0 0 0 290 290 290 391.5 391.5 391.5 90.0 90.0 90.0 X Y Z -0.109405376 0.4307079 0.00040084976 0.00539636 1.35 1.35 1.35 0.0452 AUTHOR Postprocessed map of Elongator catalytic subcomplex Elp123 lobe from yeast at 3.3 A resolution. 5M2N B PDB experimental model 5CQS A 932-1349 PDB experimental model FLEXIBLE FIT REAL 5CQS D PDB experimental model emd_4571_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 290 290 290 0 0 0 290 290 290 391.5 391.5 391.5 90.0 90.0 90.0 X Y Z -29.129967000000001 31.765105999999999 0.0006985099 0.61996967 1.35 1.35 1.35 AUTHOR LocScale map of Elongator catalytic subcomplex Elp123 lobe used to build the atomic model. emd_4571_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 290 290 290 0 0 0 290 290 290 391.5 391.5 391.5 90.0 90.0 90.0 X Y Z -12.053444000000001 29.260445000000001 0.005517913 0.3590752 1.35 1.35 1.35 AUTHOR LocScale map of Elongator catalytic subcomplex Elp123 lobe including the dimerization domain (DD) of Elp1, used to build the atomic model of the C-terminal domains of Elp1. emd_4571_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 290 290 290 0 0 0 290 290 290 391.5 391.5 391.5 90.0 90.0 90.0 X Y Z -0.030682193 0.15467745 0.0000879843 0.0037498854 1.35 1.35 1.35 AUTHOR Half map of Elongator catalytic subcomplex Elp123 lobe from yeast. emd_4571_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 290 290 290 0 0 0 290 290 290 391.5 391.5 391.5 90.0 90.0 90.0 X Y Z -0.032715123 0.15336964 0.00008487808 0.0037596114 1.35 1.35 1.35 AUTHOR Half map of Elongator catalytic subcomplex Elp123 lobe from yeast.