3J9W

Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.

Sohmen, D.Chiba, S.Shimokawa-Chiba, N.Innis, C.A.Berninghausen, O.Beckmann, R.Ito, K.Wilson, D.N.

(2015) Nat Commun 6: 6941-6941

  • DOI: 10.1038/ncomms7941
  • Primary Citation of Related Structures:  
    3J9W

  • PubMed Abstract: 
  • Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacill ...

    Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Here we present the structure of a Gram-positive B. subtilis MifM-stalled 70S ribosome at 3.5-3.9 Å, revealing a network of interactions between MifM and the ribosomal tunnel, which stabilize a non-productive conformation of the PTC that prevents aminoacyl-tRNA accommodation and thereby induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event. Such insights expand our understanding of how the synergism between the ribosome and the nascent chain is utilized to modulate the translatome in a species-specific manner.


    Organizational Affiliation

    1] Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany [2] Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein uS2AB246Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsBBSU16490
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein uS3AC218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsCBSU01220
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein uS4AD200Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsDBSU29660
Find proteins for P21466 (Bacillus subtilis (strain 168))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein uS5AE166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsEspcABSU01330
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein bS6AF95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsFBSU40910
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Entity ID: 7
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30S ribosomal protein uS7AG156Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsGBSU01110
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Entity ID: 8
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30S ribosomal protein uS8AH132Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsHBSU01300
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Entity ID: 9
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30S ribosomal protein uS9AI130Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsIBSU01500
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Entity ID: 10
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30S ribosomal protein uS10AJ102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsJtetABSU01150
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Entity ID: 11
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30S ribosomal protein uS11AK131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsKBSU01420
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Entity ID: 12
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30S ribosomal protein uS12AL138Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsLfunstrABSU01100
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Entity ID: 13
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30S ribosomal protein uS13AM121Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsMBSU01410
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Entity ID: 14
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30S ribosomal protein uS14AN61Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsN1rpsNrpsNArpsZBSU01290
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Entity ID: 15
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30S ribosomal protein uS15AO89Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsOBSU16680
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Entity ID: 16
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30S ribosomal protein bS16AP90Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsPBSU15990
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Entity ID: 17
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30S ribosomal protein uS17AQ87Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsQBSU01250
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Entity ID: 18
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30S ribosomal protein bS18AR79Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsRBSU40890
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Entity ID: 19
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30S ribosomal protein uS19AS92Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsSBSU01200
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Entity ID: 20
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30S ribosomal protein bS20AT88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsTyqeOBSU25550
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
MifMAZ95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: mifMyqzJBSU23880
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Entity ID: 24
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50S ribosomal protein bL28B062Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmByloTBSU15820
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Entity ID: 25
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50S ribosomal protein uL29B166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmCBSU01240
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Entity ID: 26
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50S ribosomal protein uL30B259Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmDBSU01340
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Entity ID: 27
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50S ribosomal protein bL31B366Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmEBSU37070
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Entity ID: 28
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50S ribosomal protein bL32B459Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmFBSU15080
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Entity ID: 29
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50S ribosomal protein bL33B549Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmGArpmG1BSU24900
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Entity ID: 30
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50S ribosomal protein bL34B644Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmHBSU41060
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Entity ID: 31
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50S ribosomal protein bL35B766Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmIBSU28860
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Entity ID: 32
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50S ribosomal protein bL36B837Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmJBSU01400
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Entity ID: 35
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50S ribosomal protein uL2BD277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplBBSU01190
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Entity ID: 36
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50S ribosomal protein uL3BE209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplCBSU01160
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Entity ID: 37
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50S ribosomal protein uL4BF207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplDBSU01170
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Entity ID: 38
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50S ribosomal protein uL5BG179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplEBSU01280
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Entity ID: 39
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50S ribosomal protein uL6BH179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplFBSU01310
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Entity ID: 40
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50S ribosomal protein uL10BJ166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplJBSU01040
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Entity ID: 41
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50S ribosomal protein uL11BK141Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplKrelCtsp6BSU01020
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Entity ID: 42
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50S ribosomal protein uL13BM145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplMBSU01490
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Entity ID: 43
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50S ribosomal protein uL14BN122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplNBSU01260
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Entity ID: 44
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50S ribosomal protein uL15BO146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplOBSU01350
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Entity ID: 45
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50S ribosomal protein uL16BP144Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplPBSU01230
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Entity ID: 46
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50S ribosomal protein bL17BQ120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplQBSU01440
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Entity ID: 47
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50S ribosomal protein uL18BR120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplRBSU01320
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Entity ID: 48
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50S ribosomal protein bL19BS115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplSBSU16040
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Entity ID: 49
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50S ribosomal protein bL20BT119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplTBSU28850
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Entity ID: 50
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50S ribosomal protein bL21BU102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplUBSU27960
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Entity ID: 51
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50S ribosomal protein uL22BV113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplVBSU01210
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Entity ID: 52
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50S ribosomal protein uL23BW95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplWBSU01180
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Entity ID: 53
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50S ribosomal protein uL24BX103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplXBSU01270
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Entity ID: 54
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50S ribosomal protein bL27BZ94Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmABSU27940
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Entity ID: 1
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16S ribosomal RNAAA1555Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 21
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tRNA-AspAX77Bacillus subtilis subsp. subtilis str. 168
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  • Entity ID: 22
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    mRNAAY19Bacillus subtilis subsp. subtilis str. 168
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    Entity ID: 33
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    23S ribosomal RNABA2928Bacillus subtilis subsp. subtilis str. 168
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    Entity ID: 34
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    5S ribosomal RNABB119Bacillus subtilis subsp. subtilis str. 168
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2015-04-29
      Type: Initial release
    • Version 1.1: 2015-05-06
      Changes: Database references
    • Version 1.2: 2018-07-18
      Changes: Data collection