3J3W

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.7 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
  • Structures With Same Primary Citation

  • 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 s ...

    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: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32059Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmFBSU15080
Find proteins for O34687 (Bacillus subtilis (strain 168))
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Go to UniProtKB:  O34687
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2C277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplBBSU01190
Find proteins for P42919 (Bacillus subtilis (strain 168))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17N120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplQBSU01440
Find proteins for P20277 (Bacillus subtilis (strain 168))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6G179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplFBSU01310
Find proteins for P46898 (Bacillus subtilis (strain 168))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13J145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplMBSU01490
Find proteins for P70974 (Bacillus subtilis (strain 168))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14K122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplNBSU01260
Find proteins for P12875 (Bacillus subtilis (strain 168))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15L146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplOBSU01350
Find proteins for P19946 (Bacillus subtilis (strain 168))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19P115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplSBSU16040
Find proteins for O31742 (Bacillus subtilis (strain 168))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20Q119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplTBSU28850
Find proteins for P55873 (Bacillus subtilis (strain 168))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3D209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplCBSU01160
Find proteins for P42920 (Bacillus subtilis (strain 168))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21R102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplUBSU27960
Find proteins for P26908 (Bacillus subtilis (strain 168))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22S113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplVBSU01210
Find proteins for P42060 (Bacillus subtilis (strain 168))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23T95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplWBSU01180
Find proteins for P42924 (Bacillus subtilis (strain 168))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24U103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplXBSU01270
Find proteins for P0CI78 (Bacillus subtilis (strain 168))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29X66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmCBSU01240
Find proteins for P12873 (Bacillus subtilis (strain 168))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34244Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmHBSU41060
Find proteins for P05647 (Bacillus subtilis (strain 168))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15232Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplABSU01030
Find proteins for Q06797 (Bacillus subtilis (strain 168))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L116141Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplKrelCtsp6BSU01020
Find proteins for Q06796 (Bacillus subtilis (strain 168))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4E207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplDBSU01170
Find proteins for P42921 (Bacillus subtilis (strain 168))
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
ribosome RNA 23SA2927Bacillus subtilis subsp. subtilis str. 168
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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, Structure summary