Triple Stack Doxycycline Bound 50S Subunit of the Coxiella burnetii 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 2026-01-22 2026-04-22 2026-04-22 2026-04-22 Biotechnology and Biological Sciences Research Council (BBSRC) BB/M009122/1 United Kingdom Triple Stack Doxycycline Bound 50S Subunit of the Coxiella burnetii Ribosome Stuart WS Isupov MN Harmer NJ Ribosome, C. burnetii, exit tunnel, blocked, pathogen, doxycycline, triple, stack, cryo-EM, catalytic centre, inactive, antibiotic Stuart WS Isupov MN McLaren M Jenkins CH Monier A Daum B Norville IH Gold VAM Harmer NJ Triple Stack Doxycycline Bound 50S Subunit of the Coxiella burnetii Ribosome To Be Published 0353 9tz5 FULLOVERLAP EMDB EMD-56459 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 23 24 25 26 27 28 29 30 31 Coxiella burnetii NMII 23S and 5S 1 17 18 19 20 21 22 23 24 25 26 27 Coxiella burnetii NMII Ribosomal Protein 1 Coxiella burnetii NMII Coxiellacae Large Subunit Peptide (CLaSP) Coxiella burnetii NMII 0.0025300799999999997 1 LEVO MPRGRGPHGPKKFRKRNKKSR Large ribosomal subunit protein bL33 Coxiella burnetii NMII 0.008054479 1 LEVO MAVSPREKIMLQSTGKTKAGKPTGTFYTTYKNKRNTTDKLNIKKFDPRAWNSETSKCGMHVLFKEKKIPK Q83EM5 Large ribosomal subunit protein uL24 Coxiella burnetii NMII 0.011814896 1 LEVO MAIKKIKKDDTVIVITGRDKGRQGKVLKVLPNSRLLVEGINLVKKHVKPNPNKNEQGGILERELSIHVSNVAIYNPAAKK ADRVGIKTLEDGSKVRIFKSNGEVIDV Q83ER5 Large ribosomal subunit protein uL18 Coxiella burnetii NMII 0.013137419 1 LEVO MDKQEKRIRRARRTRAKIKELGAVRLCVHRSLNHIYAQLISPRDSKVLVCASTLEKEVRSQIKHGGNIQAATAIGKLIAQ RAKKAGVTKVAFDRSGYKYHGRVRALAEAVREGGIEF Q83ER0 Large ribosomal subunit protein bL36 Coxiella burnetii NMII 0.004668729 1 LEVO MKVRASVKRMCRNCKVIRRNGVVRVICSDARHKQRQKGGK Q4AAY2 5S ribosomal RNA Coxiella burnetii NMII 0.037630352 1 UUCCUGGCGGCCAUAGCGAGCGGGCCCCACCUGAUUCCAUUCCGAACUCAGAAGUGAAAACGCUUAGCGCCGAUGAUAGU GUGGGUCUCCCAUGCGAAAGUAGGUCACCGCCAGGUU CP103432.1 Large ribosomal subunit protein bL19 Coxiella burnetii NMII 0.013302429 1 LEVO MNNIIQLLETEQTQGKEIPDFRAGDTVTVQVKVKEGNRERLQAFEGVVIARRHRGLNSSFTVRKVSHGEGVERVFQLYSP LIASIKVNRRGDVRRAKLYYLRNLRGRKAKIKEKI Q83E85 Large ribosomal subunit protein uL3 Coxiella burnetii NMII 0.023547062 1 LEVO MSIGLIGRKCGMTRIFTETGSSIPVTVVEVILNRITQVKTVETDGYRAFQVAYGKKSSARVNKPLAGHYSKAAVEAGNAL REFRLGNEELTEAKAGDELKVDIFKEGQVVDVRGLTRGKGFAGTVKRHNFRTQDATHGNSLSHRAPGSIGQCQTPGRVWK GKKMAGQLGNVYCTVQSQEIIKVDVERNLLLIKGALPGAPGGEVIITQSSKKRKEDK B6J263 Large ribosomal subunit protein bL20 Coxiella burnetii NMII 0.013475972999999999 1 LEVO MPRVKRGVTARARHKKVLTKAKGYYGARSRVFRVAKQAVIKAAQYAYRDRKQRKRQFRALWIVRINAAAREHGLSYSRLI NGLMKASVAIDRKNLAELAVYDKAAFGKLAEKAKQALGG Q83C13 Large ribosomal subunit protein uL5 Coxiella burnetii NMII 0.020782402 1 LEVO MVELQELYKKTITPALQKEFGFKSVMAVPRLEKITLNMGLGEAVADKKVIERAMDDMIKISGQKPLITYARKSEAGFKIR AGWPIGCKVTLRRDRMYEFLKRLISIAIPRIRDFRGLSPKSFDGRGNYSLGIREQIVFPEIQYDKVDAIRGMDITITTTA RTDEEGRALLKAFGFPLKDESR Q83ER4 Large ribosomal subunit protein uL6 Coxiella burnetii NMII 0.019228453 1 LEVO MVSRVAKNPIKIPTGVEVNVAGQQITVKGKLGTLTRVIHRAVKVTKTDAELQTICANDSPGSNALAGTARAVLANMVQGV HTGFQRKLVMVGVGYRAKAEGKKLNLTVGLSHPVNIEMPEGITVETPSQTEIIVKGADKQRVSQVAANIREIRPPEPYKG KGIRYDNERVILKEAKKK B6J5E7 Large ribosomal subunit protein bL21 Coxiella burnetii 0.012785893999999999 1 LEVO MYAIIKTGGKQYRVTEGQMLKVEKLAQDVGQSVKFDDVLMVAAGDELHIGTPSVKDAAVTAEVVDQGRQAKIEIIKFKRR KHHMKRQGHRQDFTAVKITEIALGKAKKEVKTDGA Q83EE0 Large ribosomal subunit protein uL13 Coxiella burnetii 0.015840457999999998 1 LEVO MATYMANAKTVSPRWLLVNAEGKTLGRLASRIAAILRGKHKAEFTPHVDAGDFVVVINVDKLKVTGNKTQDKQYHHHSGY PGGLKTINFADLQAKKPQRILELAIKGMLPKGPLGRQLYRKLKIYAGDQHPHQAQQPELIDL B6J4G5 Large ribosomal subunit protein uL22 Coxiella burnetii 0.012605469999999999 1 LEVO MEVAAKLKYARISAQKARLVADQVRGLGAEQAVNLLRFSNKKAAALMKKVLDSAIANAEHNEGADIDELKVSTVMVDEGP SARRFHARARGRANQILKRTCHITVKVSDSQVEND B6J258 Large ribosomal subunit protein uL15 Coxiella burnetii 0.015320005999999999 1 LEVO MQLNDLKPAKGARHQKLRVGRGIGSGKGKTAGRGHKGQHSRAGGYHKVGFEGGQMPLQRRVPKFGFTSRKELISAEVRLG ELNKISGDVVDLASLKAANIISRQIKRVKIFAAGKLEKPVTIRGLRVTKGVKAAVEAAGGKIE B6J244 Large ribosomal subunit protein bL17 Coxiella burnetii 0.014574901999999999 1 LEVO MHHRKSGRHLNRTSAHRKAMLRNMAVSLFQHELIKTTLPKAKELRRVVEPLITLAKEDTVANRRLAFNRLRDDAIVAKLF KEIAPRHKERPGGYCRVLKYGFRNGDSAPMAIVELVDREESESSED B6J237 Large ribosomal subunit protein uL2 Coxiella burnetii 0.030481426 1 LEVO MALVKTKPTSPGRRFVVKVVHPELHKGDPYAPLVESKNRINSRNNQGRITVRRRGGGHKRNYRIIDFKRDKEGIEGKVER LEYDPNRSAHIALVLYPDGERRYIIAPKGVHKGSKVVSGREAPIRPGNCLPLQNIPLGATIHNIELKPGKGAQLVRSAGA SAQLAAKEGIYAIIRMRSGETRKILAVCRACIGEVSNSEHNLRSLGKAGAKRWRGRRPTVRGVAMNPVDHPHGGGEGKTS GGRHPVSPTGKPTKGYKTRRNKRTSNMIIRDRRKK B6J260 Large ribosomal subunit protein bL9 Coxiella burnetii 0.016603986 1 LEVO MKLILQEKVANLGNIGDQVVVKPGYARNFLLPLGKAVPATPEHIAEFEKQRAELEKAAAELLAKAKARAKKLEDKSFKIT ANASDEGRLFGSIGPREIAQAITEAGIEIEKREVDLSQGPIRQVGEYEVPLRLHTDVSVNVKIEVAPENSNS A9ND50 Large ribosomal subunit protein uL29 Coxiella burnetii 0.007717033999999999 1 LEVO MNVNDLRNKTKAELKKELLELLKEQFNLRMQKGGGEAPRPHLFKRVRRDIARVKTLLGEKERNNE B6J5E0 Large ribosomal subunit protein uL16 Coxiella burnetii 0.015532355999999999 1 LEVO MLQPSNRKYRKDFKGRNRGVASRGNRVSFGEFGLKATECARITARQLEAARRTIARHIKRGGKITIRIFPDKPITKKPLE VRQGKGKGSVEYWVALVQPGRMIFEIEGVDEALAREAFSRAAAKLPLKCLFVKRTVM B6J256 Large ribosomal subunit protein uL30 Coxiella burnetii 0.007312628999999999 1 LEVO MVQEKKLRVTLVKSKYGRKPGHRECIEGLGLRRMHQTVEVTDTPANRGMIEKVSYLLMIDEEV B6J5F0 Large ribosomal subunit protein bL25 Coxiella burnetii 0.026577008 1 LEVO MAAESFELIAELREFTGKSAARRMRRFEDKVPGTVYGAGKAPQSITLLQKDLLKALESESTFSSILTLKVGDKKQKVILK ALQRHHTKPKIVHIDFQRIKASEKLIMNVPLHFLGEDDCPGVEAGGVVSHLQSEVEIRCLPADLPEYIEVDLSHLQLDES VHLSNLKLPAGVGLTSAVDEEHDSPIASVHMPRVSKADVEAEAAEAALAKEAATEAAEEEETEKPASEAEASGEAEQADT DKKE B6J9D8 Large ribosomal subunit protein bL32 Coxiella burnetii 0.007486457 1 LEVO MAVQKSRKTRSRRGMRRSHDALRGAMLSKDPTTGETHLRHHISPEGYYKGRQILTPKESYEDEE B6J8E7 Large ribosomal subunit protein uL4 Coxiella burnetii 0.022409729 1 LEVO MELPVNSFDKKEASTLTVADSAFGSEYKEGLVHQVVNAYLAGGRAGTKAQKTRREVSGGGAKPWRQKGTGRARAGSSRSP LWRSGGVAFAAKPRDFTQKVNRKMYRSAMASILSELIRREQLVVVDSLKLNEPKTRELKESLKKLNLGNVLIIIDGDDRN INLASRNMVGVSVCDALHVDPVSLVAAENIVVTVDAVKRLEERLS A9NAM5 Large ribosomal subunit protein uL14 Coxiella burnetii 0.013564108 1 LEVO MIQTQSIVDVADNSGARRVMCIKVLGGSKRRYANIGDVIKVSIKEAIPRGKVKKGDVMHAVVVRTRKGVRRNDGSLIRFD NNAVVLLNNQLQLVGTRVFGPVVRELRTDKFMKIISLALEVL B6J5E2 Large ribosomal subunit protein bL34 Coxiella burnetii 0.005357379 1 LEVO MKRTYQPSKQKRNRTHGFRARMATKNGRQVLNRRRAKGRKRLTV B6J2B1 Large ribosomal subunit protein bL35 Coxiella burnetii 0.007415877999999999 1 LEVO MPKLKTNRGAVKRFKVTGSGKIKRAASNHNHILTKKSQKRKRRLRKIHEVAPSDMRAVSEMLRD B6J7Y0 23S ribosomal RNA Coxiella burnetii 0.947544938 1 GGUUGCAUGGUCAAGUGAAUAAGCGCAUAUGGUGGAUGCCUUGGCAGUAAGAGGCGAUGAAGGACGUAGUAGCCUGCGAU AAGCUUCGGGGAGCUGGCAAACAAGCGAUGAUCCGGAGAUUUCCGAAUGGGGAAACCCAACCUUUCGAGGUUAUCGUAUA CUGAAUUCAUAGGUAUACGAGGCGAACCUGGGGAACUGAAACAUCUAAGUACCCAGAGGAAAAGAAAUCAACCGAGAUUC CGUCAGUAGCGGCGAGCGAAAGCGGAACAGCCCAGUUACUAAAUCAUUAUUUGUUCUAGCAGAAUGUUCUGGAAAGUUCA GCCAUAGCGGGUGAUAGCCCCGUACGCGAAAGAGUAAAUAAUGUGGGUAACGAUGAGUAGGUCGGGACACGUGGUAUCUU GACUGAACAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUUACUGACCGAUAGCGAACCAGUACCGUGAGGGAAAGGU GAAAAGAACCCCGGCGAGGGGAGUGAAAUAGAACCUGAAACCGUAUGCGUACAAGCAGUAGGAGCAUUUCUUCGGAAAUG UGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUACUUGUUGUAGCGAGCUUAACCGUCUAGGGGAGGCGUAGGGAAA CCGAGUCCGAAAUGGGCGUUUAGUUGCAACGAGUAGACCCGAAACCGAGCGAUCUAUCUAUGGCCAGGGUGAAGGUCAGG UAACACUGACUGGAGGCCCGAACCCACUAAUGUUGAAAAAUUAGGGGAUGAGCUGUGGAUAGGAGUGAAAGGCUAAUCAA GCUCGGAGAUAGCUGGUUCUCCUCGAAAGCUAUUUAGGUAGCGCCUCGUGUAUGACUCUUGGGGGUAGAGCACUGUUUCG GCUAGGGGGCCAUCCCGGCCUACCAAACCGAGGCAAACUCCGAAUACCAAGAAGUUUUAGCACGGGAGACACACUGCGGG (PSU)GAUAAGGUCCGUGGUGGAAAGGGAAACAGCCCAGAUCGCCAGCUAAGGUCCCAAAAUCACAGUUAAGUGGAAAAC GAUGUGGGAAGGCUCAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAAAGCGUAAUAGCUCACUGGUCG AGUCGUCCUGCGCGGAAGAUUUAACGGGGCUCAAACUGUGUACCGAAGCUGCGGCAUCAGAAGACACUGUCUUCUGAUGG GUAGAGGAGCGUUCUGUAAGCCUGUGAAGGUGAAUCGAGAGGUUUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAG UAACGAUAAUGUGGGUGAAAAACCCACACGCCGAAAGUCUAAGGUUUCCUGCGCAACGUUAAUCGACGCAGGGUGAGUCG GCCCCUAAGGCGAGGCAGAAAUGCGUAGUCGAUGGGAAACGGGUUAAUAUUCCCGUACUUUAUAAUACUGCGAUGGGAGG ACGGAGAAGGCUAGGUCAGCCACCCGAUGGUUGUGGUGGUUUAAGUGUGUAGGAAGGGUUCUUUGGCAAAUCCGGGAACU CAAUUCCGAGACAUGAUGACGAAGUACGAACUUGUUCGUGCAAAGUGAUUGAUGCCACGCUUCCAGGAAAAGUCCCUAAG CUUCAGGUAUUGUAAAACCGUACUAUAAACCGACACAGGUGGACAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUUGGG UGAAGGAACUAGGCAAAAUGGCACCGUAACUUCGGGAGAAGGUGCGCCCUUGGUAAGUGAAGGUCCUUGCGACUGGAGCU GAAAAGGGUUGCAGAUACCAGGUGGCUGCGACUGUUUACUAAAAACACAGCACUCUGCAAACUCGUAAGAGGACGUAUAG GGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAGUGAUGGGGUUAGCCCUCGGGCGAAGCUCUUGAUCGAAGCCCCGGUAA ACGGCGGCCG(PSU)AACUA(PSU)AACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUG GCGUAACGAUAGCCACGCUGUCUCCACCCAAGACUCAGUGAAAUUGAAAUCGCUGUGAAGAUGCAGCGUACCCGCGGCUA GACGGAAAGACCCCGUGAACCUUUACUACAGCUUUACACUGAACUUUGAAUAUGCCUGUGUAGGAUAGGUGGGAGGCUUU GAAGCUGGAGCGCUAGCUCCAGUGGAGCCAACCUUGAAAUACCACCCUGGCGUGUUUGAGGUUCUAACCCUGUCCCGUAA UCCGGGUCGGGAACAGUGUAUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCCAAAAGAGUAACGGAGGAGUACAAA GGUACCCUCAGCACGGUCGGAAAUCGUGCAUUGUGUGCAAAGGCAUAAGGGUGCUUGACUGCGAGACUGACAAGUCGAGC AGGUACGAAAGUAGGUCUUAGUGAUCCGGUGGUCCUUUAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGA UAACAGGCUGAUACCACCCAAGAGUUCAUAUCGACGGUGGUGUUUGGCACCUCG(2MA)(PSU)GUCGGCUCAUCACAUC CUGGGGCUGUAGCCGGUCCCAAGGGUAUGGC(OMU)GUUCGCCAUUUAAAGUGGUACGUGAGC(PSU)GGGUUUAGAACG UCGUGAGACAGU(PSU)CGGUCCCUAUCUGCCGUGGGCGUUGGAGAUUUGAGAGGAGCUGCUCCUAGUACGAGAGGACCG GAGUGGACGUACCUCUGGUGUUCCGGUUGUCACGCCAGUGGCAUUGCCGGGUAGCUAAGUACGGACGGGAUAACCGCUGA AAGCAUCUAAGCGGGAAGCCCCCCUCAAGAUGAGAUCUCCCGGACCUUUAAGGUCCCUAAAGAUUCGUUGAAGACGACAA CGUUGAUAGGCAGGGUGUGGAAGCUCAGUAAUGAGUGAAGCUAACCUGUACUAAUUAAUCGUGCGACUUGACUAUGUAAC C Large ribosomal subunit protein bL27 Coxiella burnetii 0.010069655 1 LEVO MAHKKAGGSTRNGRDSNPKMLGVKRFGGERVLAGNIIVRQRGTHYRPGENMGMGRDHTLYALIEGKVKFTRKGPKKRNFV SIEPLEESQP B6J9K3 Large ribosomal subunit protein uL23 Coxiella burnetii 0.010828598 1 LEVO MNEERLFEILLAPHISEKGALTTGQYVFEVMPDATKPEIKRAVEKQFNVTVKSVRTCNVKGKTTRFRQVRGRRKNWKKAY VMLAPGSEIDIAAGE Q83ES2 Large ribosomal subunit protein bL28 Coxiella burnetii 0.009266986 1 LEVO MAKVCQVTGKRPQSGNNVSHANKKTNRRFLPNLKKRRFWLPDEKRFITLTVSTHGMRIIDKLGINAVLKKIREREKESK B6J5S6 ZINC ION 6.5409e-05 1 ZN MAGNESIUM ION 2.4305e-05 167 MG POTASSIUM ION 3.9098e-05 134 K (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE 0.00044443499999999997 3 DXT water 1.8015e-05 9 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 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 45.0 1 cryoSPARC 4 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio reconstruction in cryoSPARC

2.22 FSC 0.143 CUT-OFF cryoSPARC 4 91218 MAXIMUM LIKELIHOOD cryoSPARC 4 MAXIMUM LIKELIHOOD cryoSPARC 4 5 cryoSPARC 4 emd_56459.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 -0.16283551 0.55308616 0.0010716959 0.016359162 1.06 1.06 1.06 0.07 AUTHOR ::::EMDATABANK.org::::EMD-56459:::: Other in silico model

modelangelo

UCSF ChimeraX 1.9 emd_56459_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 -0.21000262 0.64215374 0.0009879424 0.030158145 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-56459:::: emd_56459_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 -0.21983448 0.64505035 0.000980085 0.030188687 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-56459::::