2024-07-24 REL PDBe PDBe PDBe 2022-06-15 2022-11-02 2022-11-02 2024-07-24 Other government DLR01KI1820 Swedish Research Council 2018-00956 Sweden Cryo-EM structure of Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit. Koller TO Crowe-McAuliffe C Wilson DN Ribosome, Listeria monocytogenes, Lincomycin, 50S, antibiotic Koller TO Turnbull KJ Vaitkevicius K Crowe-McAuliffe C Roghanian M Bulvas O Nakamoto JA Kurata T Julius C Atkinson GC Johansson J Hauryliuk V Wilson DN Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes. Nucleic Acids Res. UK 50 11285 11300 2022 36300626 doi:10.1093/nar/gkac934 1362-4962 0389 NARHAD EMD-15161 other EM volume 8a5i FULLOVERLAP Lincomycin bound to the Listeria monocytogenes 50S ribosomal subunit. Lincomycin bound to the Listeria monocytogenes 50S ribosomal 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 Listeria monocytogenes E 1 50S ribosomal protein L28 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.007010382999999999 1 LEVO MAKECVITGRKSRSGNKRSHAMNSSKRTWKANLQKVRILVNGKPKKVWVSARALKSGKVERV P66144 50S ribosomal protein L29 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.007414547999999999 1 LEVO MKANDIRDLSTTEIQDQEKALKEELFNLRFQLATGQLENTARIREVRKAIARMKTIVRERELA P66166 50S ribosomal protein L30 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.006504752999999999 1 LEVO MAKLEITLKRSLIGRPQPQRKTVQALGLGKTNSVVVKEDNPAIRGMITKVSHLVDVKEV Q927M5 50S ribosomal protein L31 type B Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.00927436 1 LEVO MKTGIHPEYRPVVFVDTSTDFKFLSGSTKSSSETIKWEDGNEYPLLRVEISSDSHPFYTGKQKHATADGRVDRFNKKYGL K P0A485 50S ribosomal protein L32-2 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.006534564 1 LEVO MAVPFRRTSKAKKRKRRTHVKLQLPGMNECSNCGEYRLSHHVCPECGQYDGKDVANS P66207 50S ribosomal protein L33 1 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.006021034 1 LEVO MRVNITLECTECGDRNYITTKNKRENPERIELKKYCPRLRRVTLHRETK P66219 50S ribosomal protein L34 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.0053194570000000005 1 LEVO MKRTYQPSKRKRKKVHGFRTRMSTKNGRRVLASRRRKGRKVLSA P66248 50S ribosomal protein L35 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.007746438 1 LEVO MPKMKTHRGSAKRFKRTGSGKLKRRHGFTSHMFANKSQKQKRKLRKSAMVSAGDFKRIRQMVAKMK P0A491 50S ribosomal protein L36 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.0043364599999999994 1 LEVO MKVRPSVKPMCEKCKVIRRKGKVMVICENPKHKQKQG P66290 23S ribosomal RNA Listeria monocytogenes EGD-e 0.9507104379999999 1 GGUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAAGAAGGACGGGACUAACACCGAUAUGCUUUG GGGAGCUGUACGUAAGCGUUGAUCCAGAGAUUUCCGAAUGGGGGAACCCACUAUCUUUAGUCGGAUAGUAUCCUUACGUG AAUACAUAGCGUGAGGAAGGCAGACCCAGGGAACUGAAACAUCUAAGUACCUGGAGGAAGAGAAAGAAAAAUCGAUUUCC UGAGUAGCGGCGAGCGAAACGGAAAGAGCCCAAACCAAGAAGCUUGCUUCUUGGGGUUGUAGGACACUCUAUAUGGAGUU ACAAAAGAAAGUUAUAAAUGAAGCGGUCUGGAAAGGCCCGCCAAAGACGGUAACAGCCCGGUAGUUGAAAUGGCUUUCCC UCCAGAGUGGAUCCUGAGUACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUACU CCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAACAGUUCCUGAAA CCGUGUGCCUACAAGUAGUUAGAGCCCGUUAAUGGGUGAUAGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUG UUGCAAGGUUAAGCGGAAAAAGCGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGCAUAAGUAACAGGUCGUAGACCCG AAACCAGGUGAUCUACCCAUGUCCAGGAUGAAGGUAAGGUAAUACUUACUGGAGGUCCGAACCCACGCACGUUGAAAAGU GCGGGGAUGAGGUGUGGGUAGCGGAGAAAUUCCAAUCGAACUUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCU AGCCUCGAGGUAAAGAGUCAUGGAGGUAGAGCACUGUUUGGACUAGGGGCCCUUCUCGGGUUACCGAAUUCAGAUAAACU CCGAAUGCCAUGUACUUAUACUCGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAAAGGGAAACAGCCCAGACCAC CAGUUAAGGUCCCCAAAUAUAUGUUAAGUGGAAAAGGAUGUGGGGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAG CCACCAUUGAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACCCCGCGCCGAAAAUGUACCGGGGCUAAACAUAUUACCG AAACUGUGGAUGAACCUCUUUAGAGGUUCGUGGUAGGAGAGCGUUCUAAGGGCGGUGAAGUCAGACCGGAAGGACUGGUG GAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAAGGGUGAGAAUCCCUUCCACCGAAUAUCUAAGGUUUCCU GAGGAAGGCUCGUCCGCUCAGGGUUAGUCGGGACCUAAGCCGAGGCCGAUAGGCGUAGGCGAUGGACAACAGGUAGAGAU UCCUGUACCAGUGCUAAUUGUUUAACCGAUGGGGUGACACAGAAGGAUAGGGAAUCGCACGAAUGGAAAUGUGCGUCCAA GCAGUGAGUGUGAGAAGUAGGCAAAUCCGCUUCUCGCGAAGCAUGAGCUGUGAUGGGGAAGGAAAUUAAGUACGGAAGUU CCUGAUUUCACGCUGUCAAGAAAAGCCUCUAGGAAGAGUAGUACUGCCCGUACCGCAAACCGACACAGGUAGAUGAGGAG AGAAUCCUAAGGUGAGCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCU AUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGCGACUGUUUAGCAAAAACACAGGUCUCUGCAAAACCG UAAGGUGACGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGCUUAGCUUCGGCGAAGGUACGAAUU GAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCAC GAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGC GACAGGACGGAAAGACCCCGUGGAGCUUUACUGCAACCUGAUAUGGAAUGUUUGUACCGCUUGUACAGGAUAGGUAGGAG CCGAAGAGACGUGUGCGCUAGCAUACGAGGAGGCAAUGGUGGGAUACUACCCUGGCUGUAUGACCAUUCUAACCCGCCAC GCUUAGCGCGUGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAGAGUAACGGAGGCGCCCAA AGGUUCCCUCAGAAUGGAUGGAAAUCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACUGACAAGUCGAG CAGGGACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGG AUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGC UGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCG GUCCCUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACACACCGCUGGU GUACCAGUUGUUCCGCCAGGAGCAUCGCUGGGUAGCUAUGUGUGGCAGGGAUAAACGCUGAAAGCAUCUAAGCGUGAAGC CCCCCUCAAGAUGAGAUUUCCCAUUUCUUCGGAAAGUAAGAUCCCUGAAAGAUGAUCAGGUAGAUAGGUUUGGAGUGGAA GUGUAGCGAUACAUGGAGCGGACAAAUACUAAUCGAUCGAGGACUUAACCA CP006591.1 5S ribosomal RNA Listeria monocytogenes EGD-e 0.03671673 1 CUGGUAGUUAUGGCGAGAAGGUCACACCCGUUCCCAUACCGAACACGGUAGUUAAGCUUCUCUGCGCCAAUGGUAGUUGG GGGCUUCCCCCUGCGAGAGUAGGUCGCUGCCGGG CP020774.1 50S ribosomal protein L2 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.030568366999999996 1 LEVO MAIKKYKPTTNGRRHMTSSDFAEITTSTPEKSLLRPLKKKAGRNNQGKLTVRHHGGGHKRQYRVIDFKRNKDGIPGRVAT IEYDPNRSANIALINYADGEKRYIIAAKGLEVGQTIYSGAEADIKVGNALELKDIPVGTVIHNIEMKPGKGGQLVRSAGT SAQVLGKEGKYVLIRLNSGEVRMILATCRATIGQVGNEQHELINIGKAGRSRWMGKRPTVRGSVMNPNDHPHGGGEGKAP IGRKSPMSPWGKPTLGYKTRKKNNNSDKFIVRRRKKK P60426 50S ribosomal protein L3 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.022863459 1 LEVO MTKGILGRKVGMTQVFTENGELIPVTVIEAAQNVVLQKKTVETDGYEAVQIGFEDKRAILSNKPEQGHVAKANTTPKRFI REFRDVNLDEYEIGAEVKVDVFAEGDIIDATGVSKGKGFQGVIKRHGQSRGPMAHGSRYHRRPGSMGPVAPNRVFKNKLL PGRMGGEQITIQNLEIVKVDVEKNVLLVKGNVPGAKKALVQIKTATKAK Q8Y440 50S ribosomal protein L4 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.022640261999999998 1 LEVO MPKLSLLKQDGTNAGEITLNDTVFGIEPNEKVVVDVILSQRASLRQGTHKVKNRSEVRGGGRKPWRQKGTGRARQGSIRS PQWRGGGVVFGPTPRSYAYKLPKKVRRLAIKSILSSKVNEEKLVVLEGLTFDAPKTKEFAAFLKNISVDTKALIVVAGES ENVELSARNLQGITVIPAESISVLEVAKHDKLIITKAAVEKVEEVLA P61055 50S ribosomal protein L5 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.020023247999999997 1 LEVO MNRLKDQYLKEIVPALMSKFNYDSVMEVPKIDKIVINTGVGDATANAKVLDSAVEELALITGQKPVITKAKNSIAGFRLR EGMPIGAKVTLRGERMYDFLDKLVTVSLPRVRDFRGVSKKAFDGRGNYTLGVREQLIFPEIDYDQVSKVRGMDVVIVTTA KSDEESHELLTQLGMPFQK Q927L9 50S ribosomal protein L6 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.019434365000000002 1 LEVO MSRIGKKTIVIPAGVTVTLNGSTATVKGPKGELVKEFNPEITIKIEGNEINVSRPTDNKNHRALHGTTRAILNNMVVGVS EGYEKKLELIGVGYRAQKQGDKLVLNVGYSHPVEFVAPKGVDIEVPANTQVIVKGYNKEHVGELAANIRAVRPPEPYKGK GIRYEGEHVRRKEGKTGK Q8Y444 50S ribosomal protein L13 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.016227671 1 LEVO MRTTYMAKPGEVERKWYVIDATGVSLGRLSSEVASILRGKNKPQFTPHIDTGDFVIIINAGKIGLTGKKATDKIYYRHSQ YPGGLKSRTAGEMRTNNPEKLLELSIKGMLPKNSLGRQLFKKLHVYGGSEHEHAAQQPEVYELRG Q8Y458 50S ribosomal protein L14 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.013248426999999998 1 LEVO MIQQESRMKVADNSGAREVLTIKVLGGSGRKTANIGDVVVCTVKQATPGGVVKKGEVVKAVIVRTKSGARRQDGSYIKFD ENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPEVL Q927L7 50S ribosomal protein L15 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.015812118 1 LEVO MKLHELKPSEGSRKERNRVGRGTGSGNGKTSGRGHKGQKARSGGGVRLGFEGGQLPLFRRIPKRGFTNINRKEFAIVNLD VLNRFEDGTEVTPELLVETGIIRNEKSGIKILSNGNIEKKLTVKANKFSAAAKEAIEAAGGKTEVI Q8Y447 50S ribosomal protein L16 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.016171043 1 LEVO MLVPKRVKYRREFRGNMRGRAKGGTEVAFGEYGLQAVEASWITNRQIEAARIAMTRYMKRGGKVWIKIFPHKSYTSKPIG VRMGKGKGAPEGWVSPVKRGKIMFEIAGVPEDVAREALRLAAHKLPVKTKIVKREEIGGEANES Q927L4 50S ribosomal protein L17 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.015246793 1 LEVO MGYRKLGRTSSQRKALLRDLATDLIVFERIETTEARAKEIRKVVEKLITSGKKGDLHARRQAAAFIRHEVVEVVQVDAKG KDGSTVKKNRPVYALQKLFDDVAPRYAERQGGYTRILKKGPRRGDGAPMVIIELV Q8Y450 50S ribosomal protein L18 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.013121935999999999 1 LEVO MITKIDKNKVRKKRHARVRSKISGTESRPRLNVFRSNKNIYAQIIDDVNGVTLASASNLDKDFGSAESKVDAASKVGELV AKRASEKGITSVTFDRGGYLYHGRVKALAEAARENGLEF Q8Y445 50S ribosomal protein L19 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.013146462999999999 1 LEVO MNKLIDEITKSQLNPDVPNFRPGDTVRVHAKVVEGTRERIQLFEGVVIKRRGAGISETFTVRKISNSVGVERTFPVHTPR IAKLEVIRRGKVRRAKLYYLRNLRGKAARIKEIR O53083 50S ribosomal protein L20 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.01371935 1 LEVO MPRVKGGTVTRKRRKKIVKLAKGYYGSKHLLFKVANQAVMKSYQYAYRDRRQKKRDFRRLWIARINAAARMQDLSYSKLM HGLKLAGIDINRKMLADLAVNDIASFNTLADSAKKALAK P66103 50S ribosomal protein L21 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.011234029 1 LEVO MYAIIETGGKQIKVEAGQEIYVEKLAGEVGDVVTFDKVLFVGGDSAKVGVPFVEGATVTAKVEKQGRAKKLTVYKYKPKK NYHKKQGHRQPYTKLTIDAINA Q8Y6Y9 50S ribosomal protein L22 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.012895944999999999 1 LEVO MASEVTSAKAVAKTVRIAPRKARIVIDLIRGKQVGEAIAILKYTPRSASPIIEKVLKSAIANAEHNYDLDINNLVVEEAF VDEGPTLKRFRPRAQGRASAINKRTSHITVVVSEVKEG Q927L2 50S ribosomal protein L23 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.010935654 1 LEVO MDARDIIKRPVVTEESTSILDDKKYTFEVDTRATKTQVKYAVEEIFDVKVAKVNVMNYKGKLKRMGRYAGYTNKRRKAIV TVTADSKEIQFFEV Q8Y441 50S ribosomal protein L24 Listeria monocytogenes EGD-e 0.011205304 1 LEVO MHVKKGDKVKVITGKDKGKSGKVLAAFPKKDRVLIEGINMVKKHTKPSNVNPQGGILNVEAPIHVSNVMLLDPKTGEPTR VGYEVKGDKKVRVAKKSGEVIDK A0A0P6T4V2 50S ribosomal protein L27 Listeria monocytogenes EGD-e ATCC BAA-679 / EGD-e 0.01057193 1 LEVO MLKFDIQHFAHKKGGGSTSNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGTNVGRGGDDTLFAKTDGVVRFERM GRDKKKVSVYPEVQEA P66125 ZINC ION 6.5409e-05 2 ZN SPERMIDINE 0.000145246 1 SPD MAGNESIUM ION 2.4305e-05 165 MG 1,4-DIAMINOBUTANE 8.815099999999999e-05 2 PUT LINCOMYCIN 0.00040653699999999995 1 3QB POTASSIUM ION 3.9098e-05 1 K water 1.8015e-05 1381 HOH singleParticle particle 7.5 20.0 C8H18N2O4S HEPES 15.0 Mg(OAc)2 Magnesium acetate 95.0 KCl Potassium chloride 5.0 NH4Cl Ammonium chloride 0.5 CaCl2 Calcium chloride 8.0 C4H12N2 Putrescine 1.0 C7H19N3 Spermidine 0.5 C10H16N2O8 EDTA
0.05% Nikkol
 Quantifoil R2/2 COPPER CARBON CONTINUOUS 2.0 ETHANE-PROPANE 100 277 FEI VITROBOT MARK IV
5 OD260/mL
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.4 1.4000000000000001 270000.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 40.3 1 506262 7NHN
Listeria monocytogenes 70S
 1 FOURIER SPACE 2.3 FSC 0.143 CUT-OFF 285330 ANGULAR RECONSTITUTION RELION 3.1.3 ANGULAR RECONSTITUTION RELION 3.1.3 6 100000.0 RELION 3.1.3 emd_15175.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 309.0 309.0 309.0 90.0 90.0 90.0 X Y Z -0.2238391 0.43268916 0.00059460243 0.01273682 0.7725 0.7725 0.7725 0.03 AUTHOR Post-processed masked final map. emd_15175_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 309.0 309.0 309.0 90.0 90.0 90.0 X Y Z -0.029518869 0.10063979 0.000017627119 0.0040229405 0.7725 0.7725 0.7725 AUTHOR Final 3D refined map. emd_15175_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 309.0 309.0 309.0 90.0 90.0 90.0 X Y Z -0.041769024 0.110477835 0.000018300754 0.005755645 0.7725 0.7725 0.7725 AUTHOR Half-map 1. emd_15175_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 309.0 309.0 309.0 90.0 90.0 90.0 X Y Z -0.039749775 0.11229413 0.000016925404 0.0057522072 0.7725 0.7725 0.7725 AUTHOR Half-map2.