5ZEP

M. smegmatis hibernating state 70S ribosome structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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

    NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsOMSMEG_2654MSMEI_2591
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
98Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsQMSMEG_1445MSMEI_1409
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18 2
r
84Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsR2rpsR1MSMEG_6895MSMEI_6711
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
93Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsSMSMEG_1440MSMEI_1404
Find proteins for A0QSD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
86Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsTMSMEG_4571MSMEI_4459
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
61Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsZrpsNMSMEG_1468MSMEI_1432
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
277Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsBMSMEG_2519MSMEI_2460
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
201Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsDMSMEG_1523MSMEI_1487
Find proteins for A0QSL7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
96Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Find proteins for A0A0D6J3X3 (Mycolicibacterium smegmatis)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
124Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsMMSMEG_1521MSMEI_1485
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
275Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsCMSMEG_1442MSMEI_1406
Find proteins for A0QSD7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
156Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsPMSMEG_2435MSMEI_2374
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Conserved domain protein
u
33Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: MSMEG_0945
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promoting factor
x
230Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: hpfMSMEG_1878
Find proteins for A0QTK6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
bS1
0
479Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
278Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplBMSMEG_1439MSMEI_1403
Find proteins for A0QSD4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
217Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplCMSMEG_1436MSMEI_1400
Find proteins for A0QSD1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
215Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplDMSMEG_1437MSMEI_1401
Find proteins for A0QSD2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
187Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplEMSMEG_1467MSMEI_1431
Find proteins for A0QSG1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
179Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplFMSMEG_1470MSMEI_1434
Find proteins for A0QSG4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
214Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsEMSMEG_1472MSMEI_1436
Find proteins for A0QSG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
151Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplIMSMEG_6894MSMEI_6710
Find proteins for A0R7F6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
I
175Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplJMSMEG_1364MSMEI_1325
Find proteins for A0QS62 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
J
142Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplKMSMEG_1346MSMEI_1308
Find proteins for A0QS45 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
147Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplMMSMEG_1556MSMEI_1519
Find proteins for A0QSP8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
122Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplNMSMEG_1465MSMEI_1429
Find proteins for A0QSF9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
147Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplOMSMEG_1474
Find proteins for A0QSG8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
138Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplPMSMEG_1443MSMEI_1407
Find proteins for A0QSD8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
199Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplQMSMEG_1525MSMEI_1489
Find proteins for A0QSL9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
127Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplRMSMEI_1435
Find proteins for I7FGD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
113Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplSMSMEG_2440MSMEI_2379
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsGMSMEG_1399MSMEI_1361
Find proteins for A0QS97 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
129Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplTMSMEG_3791MSMEI_3703
Find proteins for A0QYU6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplUMSMEG_4625MSMEI_4508
Find proteins for A0R151 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
153Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplVMSMEG_1441MSMEI_1405
Find proteins for A0QSD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
100Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplWMSMEG_1438MSMEI_1402
Find proteins for A0QSD3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
105Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplXMSMEG_1466MSMEI_1430
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
215Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rplYctcMSMEI_5282
Find proteins for I7GFB2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
88Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmAMSMEG_4624MSMEI_4507
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
64Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmB-3rpmBMSMEI_2340
Find proteins for I7FJ52 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
77Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmCMSMEG_1444MSMEI_1408
Find proteins for A0QSD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
v
61Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmDMSMEG_1473MSMEI_1437
Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
132Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsHMSMEG_1469MSMEI_1433
Find proteins for A0QSG3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
y
75Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmEMSMEG_4951MSMEI_4823
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
z
57Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmFMSMEG_5489MSMEI_5337
Find proteins for A0R3I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 1
1
55Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmG1rpmG2MSMEG_1339MSMEI_1301
Find proteins for A0QS39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
47Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmHMSMEG_6946MSMEI_6752
Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmIMSMEG_3792MSMEI_3704
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
37Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpmJMSMEG_1520MSMEI_1484
Find proteins for A0QSL4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
5
24Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: MSMEG_1916
Find proteins for A0QTP4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
150Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsIMSMEG_1557MSMEI_1520
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
101Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsJMSMEG_1435MSMEI_1399
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
138Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsKMSMEG_1522MSMEI_1486
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Mycobacterium smegmatis str. MC2 155Mutation(s): 0 
Gene Names: rpsLMSMEG_1398MSMEI_1360
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAa1528Mycobacterium smegmatis str. MC2 155

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Entity ID: 22
MoleculeChainsLengthOrganism
E-tRNAfMetw77Escherichia coli

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Entity ID: 57
MoleculeChainsLengthOrganism
5S rRNAB118Mycobacterium smegmatis str. MC2 155

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Entity ID: 58
MoleculeChainsLengthOrganism
23S rRNAA3120Mycobacterium smegmatis str. MC2 155
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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