5O61

The complete structure of the Mycobacterium smegmatis 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.

Hentschel, J.Burnside, C.Mignot, I.Leibundgut, M.Boehringer, D.Ban, N.

(2017) Cell Rep 20: 149-160

  • DOI: 10.1016/j.celrep.2017.06.029
  • Primary Citation of Related Structures:  
    5O61, 5O60, 5O5J

  • PubMed Abstract: 
  • The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance ...

    The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL37 324Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1916
Find proteins for A0QTP4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 C278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplBMSMEG_1439MSMEI_1403
Find proteins for A0QSD4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 D217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplCMSMEG_1436MSMEI_1400
Find proteins for A0QSD1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 E215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplDMSMEG_1437MSMEI_1401
Find proteins for A0QSD2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 F187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplEMSMEG_1467MSMEI_1431
Find proteins for A0QSG1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 G179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplFMSMEG_1470MSMEI_1434
Find proteins for A0QSG4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 H151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplIMSMEG_6894MSMEI_6710
Find proteins for A0R7F6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10 I175Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplJMSMEG_1364MSMEI_1325
Find proteins for A0QS62 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11 J142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplKMSMEG_1346MSMEI_1308
Find proteins for A0QS45 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 K147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplMMSMEG_1556MSMEI_1519
Find proteins for A0QSP8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
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50S ribosomal protein L14 L122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplNMSMEG_1465MSMEI_1429
Find proteins for A0QSF9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 M147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplOMSMEG_1474
Find proteins for A0QSG8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 N138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplPMSMEG_1443MSMEI_1407
Find proteins for A0QSD8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 O199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplQMSMEG_1525MSMEI_1489
Find proteins for A0QSL9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 17
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50S ribosomal protein L18 P127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplRMSMEG_1471
Find proteins for A0QSG5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 Q113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplSMSMEG_2440MSMEI_2379
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 R129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplTMSMEG_3791MSMEI_3703
Find proteins for A0QYU6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21 S103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplUMSMEG_4625MSMEI_4508
Find proteins for A0R151 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 T153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplVMSMEG_1441MSMEI_1405
Find proteins for A0QSD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23 U100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplWMSMEG_1438MSMEI_1402
Find proteins for A0QSD3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24 V105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplXMSMEG_1466MSMEI_1430
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 W215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rplYctcMSMEG_5431
Find proteins for A0R3D2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27 X88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmAMSMEG_4624MSMEI_4507
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
LSU ribosomal protein L28P Y64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmBMSMEG_2400
Find proteins for A0QV03 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 Z77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmCMSMEG_1444MSMEI_1408
Find proteins for A0QSD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 a61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmDMSMEG_1473MSMEI_1437
Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 b57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmFMSMEG_5489MSMEI_5337
Find proteins for A0R3I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 1 c55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmG1rpmG2MSMEG_1339MSMEI_1301
Find proteins for A0QS39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 d47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmHMSMEG_6946MSMEI_6752
Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 32
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50S ribosomal protein L35 e64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmIMSMEG_3792MSMEI_3704
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 f37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmJMSMEG_1520MSMEI_1484
Find proteins for A0QSL4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 g75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_4951MSMEI_4823
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved domain protein BB33Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0945
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 BC275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsCMSMEG_1442MSMEI_1406
Find proteins for A0QSD7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 BD201Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsDMSMEG_1523MSMEI_1487
Find proteins for A0QSL7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 39
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30S ribosomal protein S5 BE214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsEMSMEG_1472MSMEI_1436
Find proteins for A0QSG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 40
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30S ribosomal protein S6 BF96Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Find proteins for A0A0D6J3X3 (Mycolicibacterium smegmatis)
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Entity ID: 41
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30S ribosomal protein S7 BG156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsGMSMEG_1399MSMEI_1361
Find proteins for A0QS97 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 42
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30S ribosomal protein S8 BH132Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsHMSMEG_1469MSMEI_1433
Find proteins for A0QSG3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 43
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30S ribosomal protein S9 BI150Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsIMSMEG_1557MSMEI_1520
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 44
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30S ribosomal protein S10 BJ101Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsJMSMEG_1435MSMEI_1399
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 45
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30S ribosomal protein S11 BK138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsKMSMEG_1522MSMEI_1486
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 46
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30S ribosomal protein S12 BL124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsLMSMEG_1398MSMEI_1360
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 47
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30S ribosomal protein S13 BM124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsMMSMEG_1521MSMEI_1485
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 48
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30S ribosomal protein S14 type Z BN61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsZrpsNMSMEG_1468MSMEI_1432
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 49
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30S ribosomal protein S15 BO89Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsOMSMEG_2654MSMEI_2591
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 BP156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsPMSMEG_2435MSMEI_2374
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 BQ98Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsQMSMEG_1445MSMEI_1409
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 2 BR84Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsR2rpsR1MSMEG_6895MSMEI_6711
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 BS93Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsSMSMEG_1440MSMEI_1404
Find proteins for A0QSD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 BT86Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsTMSMEG_4571MSMEI_4459
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 BV277Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpsBMSMEG_2519MSMEI_2460
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 2
MoleculeChainsLengthOrganismImage
23S rRNAA3120Mycolicibacterium smegmatis MC2 155
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S rRNAB118Mycolicibacterium smegmatis MC2 155
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Entity ID: 35
MoleculeChainsLengthOrganismImage
16S rRNABA1528Mycolicibacterium smegmatis MC2 155
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Entity ID: 56
MoleculeChainsLengthOrganismImage
P/P-site Phe-tRNA(Phe)BW76Mycolicibacterium smegmatis MC2 155
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  • Entity ID: 57
    MoleculeChainsLengthOrganismImage
    mRNA fragmentBX6Mycolicibacterium smegmatis MC2 155
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PHE
    Query on PHE

    Download Ideal Coordinates CCD File 
    BW
    PHENYLALANINE
    C9 H11 N O2
    COLNVLDHVKWLRT-QMMMGPOBSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    BN, BR, Y, c, f, g
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    A, B, BA, BF, BR, C, F, M, N, T, c
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.31 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Swiss National Science FoundationSwitzerland310030B_163478
    NCCR RNA and disease program, SNSFSwitzerland51NF40_141735

    Revision History  (Full details and data files)

    • Version 1.0: 2017-07-12
      Type: Initial release
    • Version 1.1: 2017-07-19
      Changes: Database references