5ZEU

M. smegmatis P/P state 30S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.

Mishra, S.Ahmed, T.Tyagi, A.Shi, J.Bhushan, S.

(2018) Sci Rep 8: 13587-13587

  • DOI: 10.1038/s41598-018-31850-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand ...

    Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.


    Organizational Affiliation

    Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
275Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsC
Find proteins for A0QSD7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
214Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsE
Find proteins for A0QSG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsG
Find proteins for A0QS97 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS97
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
132Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsH
Find proteins for A0QSG3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
150Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsI
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSP9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
101Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
138Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsK
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL6
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsL
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS96
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsO
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QVQ3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
98Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSE0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18 2
r
84Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsR2 (rpsR1)
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7F7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
93Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsS
Find proteins for A0QSD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
86Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsT
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R102
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
61Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG2
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
277Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsB
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QVB8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
201Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsD
Find proteins for A0QSL7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
96Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: rpsF
Find proteins for A0A0D6J3X3 (Mycolicibacterium smegmatis)
Go to UniProtKB:  A0A0D6J3X3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
124Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsM
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL5
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
156Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsP
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV37
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Conserved domain protein
u
33Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QR10
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAa1528Mycolicibacterium smegmatis MC2 155
Entity ID: 15
MoleculeChainsLengthOrganism
P-tRNAfMetv77Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)Singapore--

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2019-11-06
    Type: Data collection, Other