5ZEB

M. Smegmatis P/P state 70S ribosome structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
278Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplB
Find proteins for A0QSD4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD4
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
217Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplC
Find proteins for A0QSD1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD1
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
215Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplD
Find proteins for A0QSD2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
187Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplE
Find proteins for A0QSG1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG1
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
179Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplF
Find proteins for A0QSG4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
151Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplI
Find proteins for A0R7F6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7F6
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
I
175Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplJ
Find proteins for A0QS62 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS62
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
J
142Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplK
Find proteins for A0QS45 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS45
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
147Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplM
Find proteins for A0QSP8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSP8
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
122Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplN
Find proteins for A0QSF9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSF9
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
147Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplO
Find proteins for A0QSG8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
138Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplP
Find proteins for A0QSD8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD8
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
199Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplQ
Find proteins for A0QSL9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL9
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
127Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplR
Find proteins for A0QSG5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG5
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
113Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplS
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV42
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
129Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplT
Find proteins for A0QYU6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYU6
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplU
Find proteins for A0R151 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R151
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
153Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplV
Find proteins for A0QSD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD6
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
100Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplW
Find proteins for A0QSD3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD3
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
105Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplX
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG0
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
215Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for A0R3D2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3D2
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
88Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmA
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R150
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
64Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmB
Find proteins for A0QV03 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV03
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
77Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmC
Find proteins for A0QSD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
1
61Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmD
Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG7
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
2
75Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmE
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R215
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
3
57Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmF
Find proteins for A0R3I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3I9
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 1
4
55Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmG1 (rpmG2)
Find proteins for A0QS39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS39
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
5
47Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmH
Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7K0
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
6
64Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmI
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYU7
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
7
37Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0QSL4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL4
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein bL37
8
24Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Find proteins for A0QTP4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QTP4
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAa1528Mycolicibacterium smegmatis MC2 155
Entity ID: 15
MoleculeChainsLengthOrganism
P-tRNAfMetv77Escherichia coli
Entity ID: 47
MoleculeChainsLengthOrganism
5S rRNAB118Mycolicibacterium smegmatis MC2 155
Entity ID: 48
MoleculeChainsLengthOrganism
23S rRNAA3120Mycolicibacterium smegmatis MC2 155
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 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