3J3V

Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.3 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

Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit

Li, N.Chen, Y.Guo, Q.Zhang, Y.Yuan, Y.Ma, C.Deng, H.Lei, J.Gao, N.

(2013) Nucleic Acids Res 41: 7073-7083

  • DOI: 10.1093/nar/gkt423
  • Primary Citation of Related Structures:  
    3J3V, 3J3W

  • PubMed Abstract: 
  • Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant bacterial strain ...

    Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant bacterial strain. Our qualitative mass spectrometry data indicate that L28, L16, L33, L36 and L35 are dramatically underrepresented in the 45S particles. This protein spectrum shows interesting similarity to many qualitatively analyzed 50S precursors from different genetic background, indicating the presence of global rate-limiting steps in the late-stage assembly of 50S subunit. Our structural data reveal two major intermediate states for the 45S particles. Consistently, both states severally lack those proteins, but they also differ in the stability of the functional centers of the 50S subunit, demonstrating that they are translationally inactive. Detailed analysis indicates that the orientation of H38 accounts for the global conformational differences in these intermediate structures, and suggests that the reorientation of H38 to its native position is rate-limiting during the late-stage assembly. Especially, H38 plays an essential role in stabilizing the central protuberance, through the interaction with the 5S rRNA, and the correctly orientated H38 is likely a prerequisite for further maturation of the 50S subunit.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmFBSU15080
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Entity ID: 2
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50S ribosomal protein L34B [auth 2]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmHBSU41060
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth 5]232Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplABSU01030
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11D [auth 6]141Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplKrelCtsp6BSU01020
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Entity ID: 7
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50S ribosomal protein L2G [auth C]277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplBBSU01190
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3H [auth D]209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplCBSU01160
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Entity ID: 9
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50S ribosomal protein L4I [auth E]207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplDBSU01170
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5J [auth F]179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplEBSU01280
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Entity ID: 11
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50S ribosomal protein L6K [auth G]179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplFBSU01310
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Entity ID: 12
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50S ribosomal protein L13L [auth J]145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplMBSU01490
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Entity ID: 13
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50S ribosomal protein L14M [auth K]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplNBSU01260
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Entity ID: 14
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50S ribosomal protein L15N [auth L]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplOBSU01350
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Entity ID: 15
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50S ribosomal protein L17O [auth N]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplQBSU01440
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth O]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplRBSU01320
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Entity ID: 17
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50S ribosomal protein L19Q [auth P]115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplSBSU16040
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Entity ID: 18
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50S ribosomal protein L20R [auth Q]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplTBSU28850
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Entity ID: 19
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50S ribosomal protein L21S [auth R]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplUBSU27960
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Entity ID: 20
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50S ribosomal protein L22T [auth S]113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplVBSU01210
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Entity ID: 21
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50S ribosomal protein L23U [auth T]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplWBSU01180
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Entity ID: 22
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50S ribosomal protein L24V [auth U]103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplXBSU01270
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth X]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmCBSU01240
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth Y]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmDBSU01340
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Entity ID: 5
MoleculeChainsLengthOrganismImage
ribosome RNA 23SE [auth A]2927Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 6
MoleculeChainsLengthOrganismImage
ribosome RNA 5SF [auth B]119Bacillus subtilis subsp. subtilis str. 168
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Data collection, Database references