6WNT

50S ribosomal subunit without free 5S rRNA and perturbed PTC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly.

Huang, S.Aleksashin, N.A.Loveland, A.B.Klepacki, D.Reier, K.Kefi, A.Szal, T.Remme, J.Jaeger, L.Vazquez-Laslop, N.Korostelev, A.A.Mankin, A.S.

(2020) Nat Commun 11: 2900-2900

  • DOI: 10.1038/s41467-020-16694-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whet ...

    5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA. shura@uic.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
b
271Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
c
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
d
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
f
176Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
g
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
h
131Escherichia coliMutation(s): 0 
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
i
141Escherichia coliMutation(s): 0 
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
j
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
k
122Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
l
143Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
n
120Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
p
114Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
q
117Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
r
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
s
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
t
93Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
u
102Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
v
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
w
75Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
x
77Escherichia coliMutation(s): 0 
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
y
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
z
58Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
A
70Escherichia coliMutation(s): 0 
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B
56Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
D
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
E
64Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
F
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
a
223Escherichia coliMutation(s): 0 
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
o
116Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
e
177Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
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Entity ID: 31
MoleculeChainsLengthOrganism
23s-5s joint ribosomal RNA43031Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127134
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127094
Estonian Research CouncilEstoniaPUT669
National Aeronautic Space Administration (NASA, United States)United States80NSSC17K0031

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release