T.thermophilus 30S ribosome with KsgA, class K6

2024-06-12 REL PDBj PDBj PDBj 2021-08-09 2022-04-06 2022-04-06 2024-06-12 Department of Biotechnology (DBT, India) DBT/PR12422/MED/31/287/2014 India Science and Engineering Research Board (SERB) RJN-094/2017 India Department of Biotechnology (DBT, India) IA/S/19/1/504293 India T.thermophilus 30S ribosome with KsgA, class K6 Raina R Singh J 30S subunit, KsgA, rRNA methyltransferase, RIBOSOME Singh J Raina R Vinothkumar KR Anand R Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases. Acs Chem.Biol. US 17 829 839 2022 35316014 doi:10.1021/acschembio.1c00732 1554-8937 EMD-31655 other EM volume

Different class from the same data set

EMD-31656 other EM volume

Different class from the same data set

EMD-31657 other EM volume

Different class from the same data set

EMD-31658 other EM volume

Different class from the same data set

EMD-31659 other EM volume

Different class from the same data set

7v2q FULLOVERLAP 30S ribosomal with bound KsgA, a RNA methyltransferase 30S ribosomal with bound KsgA, a RNA methyltransferase 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

30S ribosomal subunit purified from delta KsgA strain and KsgA recombinantly purified has been added after isolation for complex formation

0.74 30S ribosomal subunit 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 Thermus thermophilus HB8 KsgA 1 21 Bacillus subtilis (strain 168) 16s ribosomal RNA Thermus thermophilus HB8 0.493958281 1 UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGU UUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUC GGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAU CAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUG AGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCU UGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUA AUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGG GCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGAC GGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCC ACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAA CGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAG GCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUU ACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUG GCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUC GGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCC UGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCC AGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUA CGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGG CGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUU CU M26923.1 30S ribosomal protein S2 Thermus thermophilus HB8 0.029317703 1 LEVO MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDI VRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPD AIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ EAEATETPEGESEVEA P80371 30S ribosomal protein S3 Thermus thermophilus HB8 0.026751076 1 LEVO MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRG GERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGA EQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE P80372 30S ribosomal protein S4 Thermus thermophilus HB8 0.024373447 1 LEVO MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFE EASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQ NLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR P80373 30S ribosomal protein S5 Thermus thermophilus HB8 0.017583416 1 LEVO MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEI EVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQA QG Q5SHQ5 30S ribosomal protein S6 Thermus thermophilus HB8 0.011988753 1 LEVO MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR IRDNVRRVMVVKSQEPFLANA Q5SLP8 30S ribosomal protein S7 Thermus thermophilus HB8 0.018050973 1 LEVO MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRV GGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW P17291 30S ribosomal protein S8 Thermus thermophilus HB8 0.01586857 1 LEVO MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVI HHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW P0DOY9 30S ribosomal protein S9 Thermus thermophilus HB8 0.014410613999999999 1 LEVO MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLG IARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR P80374 30S ribosomal protein S10 Thermus thermophilus HB8 0.011954968 1 LEVO MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRK TIEQLMTLDLPTGVEIEIKTVGGGR Q5SHN7 30S ribosomal protein S11 Thermus thermophilus HB8 0.013737868 1 LEVO MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSV DVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS P80376 30S ribosomal protein S12 Thermus thermophilus HB8 0.014637384 1 LEVO MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVV LIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK Q5SHN3 30S ribosomal protein S13 Thermus thermophilus HB8 0.014338861 1 LEVO MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK P80377 30S ribosomal protein S14 type Z Thermus thermophilus HB8 0.007158725 1 LEVO MARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW P0DOY6 30S ribosomal protein S15 Thermus thermophilus HB8 0.010578406999999998 1 LEVO MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRA LIEKLGIRG Q5SJ76 30S ribosomal protein S16 Thermus thermophilus HB8 0.010409983 1 LEVO MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVF RQEAREGA Q5SJH3 30S ribosomal protein S17 Thermus thermophilus HB8 0.012325655 1 LEVO MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESG RMDLVEKYLIRRQNYESLSKRGGKA P0DOY7 30S ribosomal protein S18 Thermus thermophilus HB8 0.010258299 1 LEVO MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLP FTEKLVRK Q5SLQ0 30S ribosomal protein S19 Thermus thermophilus HB8 0.010605464 1 LEVO MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTY RGHGKEAKATKKK Q5SHP2 30S ribosomal protein S20 Thermus thermophilus HB8 0.011736143 1 LEVO MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARR KSRLMRKVRQLLEAAGAPLIGGGLSA P80380 Ribosomal RNA small subunit methyltransferase A Bacillus subtilis (strain 168) 0.033588811999999996 2 Escherichia coli BL21(DE3) LEVO HHHHHHMNKDIATPIRTKEILKKYGFSFKKSLGQNFLIDTNILNRIVDHAEVTEKTGVIEIGPGIGALTEQLAKRAKKVV AFEIDQRLLPILKDTLSPYENVTVIHQDVLKADVKSVIEEQFQDCDEIMVVANLPYYVTTPIIMKLLEEHLPLKGIVVML QKEVAERMAADPSSKEYGSLSIAVQFYTEAKTVMIVPKTVFVPQPNVDSAVIRLILRDGPAVDVENESFFFQLIKASFAQ RRKTLLNNLVNNLPEGKAQKSTIEQVLEETNIDGKRRGESLSIEEFAALSNGLYKALF P37468 2.1.1.182 30S ribosomal protein Thx Thermus thermophilus HB8 0.00335003 1 LEVO MGKGDRRTRRGKIWRGTYGKYRPRKKK Q5SIH3 ZINC ION 6.5409e-05 2 ZN singleParticle particle 7.5 50.0 Hepes 40.0 Ammonium chloride 4.0 Magensium acetate 6.0 Beta mercaptoethanol Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277.15 FEI VITROBOT MARK IV

After application of the complex, 15 seconds wait time was given before blotting..

~2 micromolar concentration of ribosome+KsgA was used during freezing

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.8 3.5 59000.0 101449.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 4096 4096 1 2.0 43.0

Total number of frames is 30. Each frame had 1.43 e/A2

1 1 C1 3.24 FSC 0.143 CUT-OFF RELION 3.1 75667 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 emd_31660.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 X Y Z -0.09327221 0.40405607 -0.0000038661024 0.013828878 1.38 1.38 1.38 0.07 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: B-factor sharpened map from the postprocess routine in Relion 4B3R PDB experimental model OTHER

Phenix was used in real space for initial refinement. The final refinements was performed with REFMAC within ccpem

RECIPROCAL 103.700000000000003 emd_31660_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 X Y Z 0.0 24.80875 0.20399062 0.7887289 1.38 1.38 1.38 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: This map was calculated using LocSpiral. This map was used in model building. emd_31660_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 Z Y X -6.8035846 29.893630000000002 0.007525758 1.0285183 1.38 1.38 1.38 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: Composite map of the multibody refinement from Phenix software. This map was used in model building. emd_31660_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 X Y Z -0.1255084 0.420652 0.0006505828 0.00833313 1.38 1.38 1.38 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: One of the maps from multibody refinement from Relion. This map was used in model building. emd_31660_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 X Y Z -0.10013319 0.40317968 0.0003577278 0.0060181245 1.38 1.38 1.38 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: One of the maps from multibody refinement from Relion. This map was used in model building. emd_31660_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 X Y Z -0.07426003 0.25766906 0.00014606505 0.0033358638 1.38 1.38 1.38 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: One of the maps from multibody refinement from Relion. This map was used in model building. emd_31660_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 X Y Z -0.027297113 0.24602732 -0.000004838713 0.008607541 1.38 1.38 1.38 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: One of the half maps from 3D refine, used in the postprocess routine to obtain the primary map. emd_31660_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 441.6 441.6 441.6 90.0 90.0 90.0 X Y Z -0.02875376 0.24376753 -0.0000028931054 0.008629001 1.38 1.38 1.38 AUTHOR ::::EMDATABANK.org::::EMD-31660:::: One of the half maps from 3D refine, used in the postprocess routine to obtain the primary map.