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 1.1 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:  

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
59Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmF
Find proteins for O34687 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34687
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
44Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmH
Find proteins for P05647 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05647
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
5
232Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q06797 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q06797
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
6
141Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplK (relC, tsp6)
Find proteins for Q06796 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q06796
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
277Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplB
Find proteins for P42919 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42919
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplC
Find proteins for P42920 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42920
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
207Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplD
Find proteins for P42921 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42921
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplE
Find proteins for P12877 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12877
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
179Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplF
Find proteins for P46898 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46898
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
145Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplM
Find proteins for P70974 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P70974
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplN
Find proteins for P12875 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12875
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
146Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplO
Find proteins for P19946 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19946
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P20277 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P20277
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplR
Find proteins for P46899 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P46899
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplS
Find proteins for O31742 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31742
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
119Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplT
Find proteins for P55873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P55873
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
102Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplU
Find proteins for P26908 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P26908
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
113Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplV
Find proteins for P42060 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42060
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
95Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplW
Find proteins for P42924 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42924
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rplX
Find proteins for P0CI78 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P0CI78
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
X
66Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P12873 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12873
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Y
59Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P19947 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19947
Entity ID: 5
MoleculeChainsLengthOrganism
ribosome RNA 23SA2927Bacillus subtilis subsp. subtilis str. 168
Entity ID: 6
MoleculeChainsLengthOrganism
ribosome RNA 5SB119Bacillus subtilis subsp. subtilis str. 168
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references