HPFcold Bound Hibernating C. burnetii 30S Ribosome

2026-04-22 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-10-20 2026-04-22 2026-04-22 2026-04-22 Biotechnology and Biological Sciences Research Council (BBSRC) BB/M009122/1 United Kingdom HPFcold Bound Hibernating C. burnetii 30S Ribosome Stuart WS Isupov MN Harmer NJ Ribosome, C. burnetii, 30S subunit, cold shock domain, pathogen, ribosomal peptide, hibernation, cryo-EM Stuart WS Isupov MN McLaren M Jenkins CH Monier A Daum B Norville IH Gold VAM Harmer NJ HPFcold Bound Hibernating C. burnetii 30S Ribosome To Be Published 0353 9t0z FULLOVERLAP PDB 9SX2 unspecified PDB 9ST6 unspecified PDB 9SLG unspecified EMDB EMD-55416 associated EM volume

Coxiella Ribosome 50S Subunit Coxiella Ribosome 50S Subunit 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Coxiella burnetii NMII 16S 1 17 18 19 20 21 22 Coxiella burnetii NMII Ribosomal Protein 1 Coxiella burnetii NMII Small ribosomal subunit protein uS13 Coxiella burnetii NMII 0.013420679 1 LEVO MAARIAGVNIPVQKHARIALQAIYGIGNSRALEICKEAKIDPATKVKDLSEAELDALRTEVGKFSVEGDLRRERSMDIKR KMDLGAYEGIRHRRGLPLRGQRTRSNARTRKGKRKPIRS P59753 Small ribosomal subunit protein uS14 Coxiella burnetii NMII 0.011599954999999999 1 LEVO MAKLSVIERNKKRVRKSQSARKKRLELKKIIKKGTPEEQEQALLKLQKRPRDESPVRTRDRCRLCGRPCGTFKKFGLCRI HLREAAMRADVPGLKKASW Q83ER3 Ribosome hibernation promoting factor Coxiella burnetii NMII 0.021176208999999998 1 LEVO MRRSFMQVPLQITLRNIDPTPAIEDRIHKKADKLSQYSDQIISCHIVVELPKRHQHQGKLYNVRINLTLPGKEFAVNRNE VEDLYVAIRNAFDDMARKVEEEMRMRMGHVKTHPELLQGEIVRLFKEKDFGFIATPDGEEFYFNAGNVVHPTFEKLEVGT TVQFIEAIGDDGAQAHRVSAKER Q83FC0 Small ribosomal subunit protein uS19 Coxiella burnetii NMII 0.010842623 1 LEVO MPRSTNKGPFVDHHLMKKVDQAQKEGSKRPIKTWSRRSMVVPEMVGLTIAIHNGRQHVPVYISENMVGHKLGEFAITRTF RAHSGDRKAKKEGEK Q83ES0 16S ribosomal RNA Coxiella burnetii NMII 0.497437656 1 AAUUGAAGAGUUUGAUUCUGGCUCAGAUUGAACGCUAGCGGCAUGCUUAACACAUGCAAGUCGAACGGCAGCGCGGGGAG CUUGCUCCCUGGCGGCGAGUGGCGGACGGGUGAGUAAUGCGUAGGAAUCUACCUUGUAGUGGGGGAUAACCUGGGGAAAC UCGGGCUAAUACCGCAUAAUCUCUUUGGAGCAAAGCGGGGGAUCUUCGGACCUCGUGCUAUAAGAUGAGCCUACGUCGGA UUAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGAUCCGUAGCUGGUCUGAGAGGACGAUCAGCCACACUGGGACU GAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGAAACCCUGAUCCAGCAAUGCCGC GUGUGUGAAGAAGGCCUUCGGGUUGUAAAGCACUUUCGGUGGGGAAGAAAUUCUCAAGGGUAAUAUCCUUGGGCGUUGAC GUUACCCACAGAAGAAGCACUGGCUAACUCUGUGCCAGCAGCC(G7M)CGGUAAUACAGAGAGUGCAAGCGUUAAUCGGA AUCACUGGGCGUAAAGCGCGCGUAGGUGGAUAUUUAAGUCGGAUGUGAAAGCCCUGGGCUUAACCUGGGAAUUGCACCCG AUACUGGGUAUCUUGAGUAUGGUAGAGGGAAGUGGAAUUUCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGAAAGAACAC CAGUGGCGAAGGCGACUUCCUGGACCAAUACUGACACUGAGGCGCGAAAGCGUGGGGAGCAAACAGGAUUAGAGACCCUG GUAGUCCACGCCGUCAACGAUGAGAACUAGCUGUUGGGAAGUUCACUUCUUAGUAGCGAAGCUAACGCGUUAAGUUCUCC GCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAGAAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU UCGAU(2MG)(5MC)AACGCGAAAAACCUUACCUACCCUUGACAUCCUCGGAACUUGUCAGAGAUGAUUUGGUGCCUUCG GGAACCGAGUGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGUAACGAGCGCAAC CCUCGUCCUUAGUUGCCAGCGAGUCAAGUCGGGAACUCUAAGGAGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGA UGUCAAGUCAUCAUGGCCCUUACGGGUAGGGCUACACACGUGCUACAAUGGGCAGUACAAAGGGUUGCCAAGCCGCGAGG UGGAGCUAAUCCCAGAAAACUGCUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUUGGAAUCGCUAGUAAU CGCGAAUCAGCAUGUCGCGGUGAAUACGUUCUCGGGCCUUGUACACACCG(4OC)CCGUCACACCAUGGGAGUGAAUUGU ACCAGAAGCGGGUAGGCUAACCUUCGGGAGGCCGCUCACCACGGUAUGAUCCAUGACUGGGGUGAAGUCG(UR3)AACAA GGUAGCCGUAGG(2MG)G(MA6)(MA6)CCUGCGGCUGGAUCACCUC Small ribosomal subunit protein uS15 Coxiella burnetii NMII 0.010340205 1 LEVO MSLASAETAKIVKEYQLGKDDTGSPEVQVAILTAKIIKLTDHMKAHKHDHHSRRGLLRMVSQRRKLLNFLKRNDLQRYLK LIERLGLRS Q83D88 Small ribosomal subunit protein uS3 Coxiella burnetii NMII 0.025671746 1 LEVO MGQKVNPVGMRIGITRDWTSNWYADKKDFADRLNEDLNVRQLLQKRLKGAAVSRIQIERPARNAKIIIHSARPGVIIGKK GGEIEALRDEIFKVMKVPVHITIEEVRKPELDAKLVAENIAQQLERRVMFRRAMKRAVQNTLRQGALGVKISVSGRLGGA EIARTEWYREGRVPLHTFRADIDYATASAKTTYGIIGVKVWIFKGEVHAPKPQAEEAAPQETEEEVK O85388 Small ribosomal subunit protein uS9 Coxiella burnetii NMII 0.015332496 1 LEVO MAQAAKKQNLGTGRRKTSSARVFLRSGTGQIIINGLPLDEYFGRETARMVVRQPLVKLDVQSRFDVYATVQGGGDSGQAG AIRHGITRALIQYDEEGGEGGTWRSTLRKAGFVTRDPRMVERKKVGLHGARRGTQFSKR Q83AX9 Small ribosomal subunit protein bS21 Coxiella burnetii NMII 0.008927503 1 LEVO MPMIDVPDNNAFDVAMRRFKRACEKAGILSKLRQIEYYEKPTSKRKRKRAAAVKRYAKKLQKEQEALERERTRY Q83BB9 Small ribosomal subunit protein bS6 Coxiella burnetii NMII 0.014603656999999999 1 LEVO MRHYEIVILVHPDQSSQVPAMVERYQSMIKEKDGKVHRLEDWGRRQLAYSIDKVHKAHYLLMNIESDQGVISELENAFRY NDAVIRSLILKRDHAITKSSLIMQGAEKGKSSRKEKVAAEAEASEEA Q83D76 Small ribosomal subunit protein bS20 Coxiella burnetii NMII 0.009981456 1 LEVO MANSAQAKKRARQNEKRELHNASQRSAVRTAVKKILKSLQANDSSAAQSAYQHAVQILDKAAGRRIIHPNKAARLKSRLS QKIKNLSSSQ Q83ED6 Small ribosomal subunit protein uS4 Coxiella burnetii NMII 0.023770687999999998 1 LEVO MARYLGPKCRLSRREKTDLQLKSGIRAIDSKCNIERIPGMHWQRRGRTTDYGVQLRMKQMIKRYYDVLEKQFANYYKQAD RLKGSTGDNLLKLLESRLDNVVYRMGFAATRAEARQLISHKAILVNGEVVNIPSYQVKPGDIIEVRSRAKGQLRIKGALE LAQQRAPISWIEVDTKKMTGTFKEQPDVAELPAEFKVNLVVELYSK Q83EQ3 Small ribosomal subunit protein uS5 Coxiella burnetii NMII 0.017510307 1 LEVO MQEAGIGTTTDGIQEKLVAVRRTAKVVKGGRVFGFSALVVAGDGDGKVGFGLGKAREVPSAIQKATENARRNMISVPLYG ATLHHAIKATHASSTVLMLPASEGTGVIAGNAMRAIFEVMGVQNVLAKCIGSSNPINVVRATFKGLKQMETPESVAAKRG KAIEEIVE Q83EQ9 Small ribosomal subunit protein uS8 Coxiella burnetii NMII 0.014592009999999999 1 LEVO MMQDPISDMLTRIRNAQAVRKKEVVMPRSKLKMSIANVLKEEGYIVDYREEGDLTKAQLVITLKYHEGESVISEIRRVSS PALQVYKSKDELPKVKNGLGIAIISTSKGVMSDRQARRLGEGGEVLCYVS Q83ER2 Small ribosomal subunit protein bS16 Coxiella burnetii NMII 0.015592906999999998 1 LEVO MVVIRLARGGSKKNPFYHIVVADRRKPRDGRFIERVGYYNPMARGQDIRLQLEKERISHWLNQGAQTSLRVKHLIKKLEK SPEEAQKGGMRKGEFKRLQAEQAAKAQKKAVATEEPKAEEAKEAPPAESQAAEGKEE Q83E83 Small ribosomal subunit protein uS12 Coxiella burnetii NMII 0.013786058999999998 1 LEVO MARINQLVRKPRRARAKKSDVPALEGCPQRRGVCTRVYTTTPKKPNSALRKVARVRITNGAEVTAYIGGEGHNLQEHSVV LIRGGRVKDLPGVRYHIVRGSLDTAGVSGRRRGRSKYGEKKPKE Q83ES9 Small ribosomal subunit protein uS17 Coxiella burnetii NMII 0.010328146 1 LEVO MNKNEKMVRSLMGTVVSNKMNDTVVVRVERRVKHPKYGKFIKRSTKIHAHDKGNEGQIGDIVTIRECRPISKTKSWTLVK INERAEKVE Q83ER7 Large ribosomal subunit protein bL31 Coxiella burnetii NMII 0.009096482999999999 1 LEVO MKENIHPPYKQIKVTCSCGNTFMTGSTLDRELHLEICSACHPFYTGQQKMVDTAGRVERFRKKYAKRRAANASPEDEKK Q83D39 Small ribosomal subunit protein uS7 Coxiella burnetii NMII 0.021334717 1 LEVO MARRKAAPKRETLPDPLFHSELLAKFINAVMRNGKKSVAEKIVYGALDVVAKRVQNKSGEQGDGDGESGGKAGGIKKRSL GDIRTDENARALALETFKGALDKVMPNVEVKSRRVGGSTYQVPVEIRMARRQALARRWLVEYANKRNEKTMVLRLAHEIL DAVEGRGGAIKKREDVHRMAKANQAFAHYKW Q83ES8 Small ribosomal subunit protein uS10 Coxiella burnetii NMII 0.012614598999999999 1 LEVO MSDNQRIRIRLKAFDHRLIDRSTREIVETARRTGAIIRGPILLPTKIERYTVLISPNIDKDARDQYEIRTHKRLVDISEP TDKTVDALMKLDLAAGVDVQIELLNKKSGA Q83ES5 Small ribosomal subunit protein uS11 Coxiella burnetii NMII 0.013534661 1 LEVO MAKKRYRKVTEGIAHIKATFNNTMISVSDPQGNVLCFRSAGGSGFKGSRKGTPYGAQMASEEVGRLARDNFDMRRIAVRV KGPGAGRDSAIRGLRSAGLEVIHLEDRTPLPHNGCRPRKKRRV Q83EQ4 Small ribosomal subunit protein bS18 Coxiella burnetii NMII 0.008569 1 LEVO MSFRRKKFCAFDAKNLQEIDYKDVNTLKDYIMESGRVVPSRITGTCAKHQRQISRAIKLARYLALLPYCDTHQ Q83D75 ZINC ION 6.5409e-05 2 ZN POTASSIUM ION 3.9098e-05 34 K MAGNESIUM ION 2.4305e-05 53 MG water 1.8015e-05 8 HOH singleParticle particle 0.05 7.5 25.0 C8H18N2O4S HEPES 100.0 KOAc Potassium Acetate 15.0 Mg(OAc) Magnesium Acetate 1.0 C4H10O2S2 DTT

BS100 ribosomal resuspension buffer

Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS 2.0 GLOW DISCHARGE ETHANE 100 298 FEI VITROBOT MARK IV

Blot time 4 s, blot force 1, blot total 1.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.0 81000.0 NITROGEN EPU

Super-resolution binned 2 in EPU

GATAN K3 (6k x 4k) 5760 4092 22295 3.0 45.0 1 cryoSPARC 4 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio reconstruction in cryoSPARC

C1 2.87 FSC 0.143 CUT-OFF cryoSPARC 4 24143 MAXIMUM LIKELIHOOD cryoSPARC 4 MAXIMUM LIKELIHOOD 2 cryoSPARC 4 emd_55416.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.07388234 0.32178324 0.002173091 0.015754847 1.06 1.06 1.06 0.07 AUTHOR ::::EMDATABANK.org::::EMD-55416:::: Local refinement of the HPFcold bound Coxiella burnetii 30S subunit following classification AlphaFold in silico model Other in silico model

Model Angelo

UCSF ChimeraX 1.9 emd_55416_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.49592257 0.5435133 0.0013670176 0.05606871 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-55416:::: emd_55416_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.4729845 0.51741713 0.0013878953 0.05556999 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-55416::::