6WNV

70S ribosome without free 5S rRNA and with a perturbed PTC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2b271Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
Explore P60422 
Go to UniProtKB:  P60422
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3c209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
Explore P60438 
Go to UniProtKB:  P60438
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5e177Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
Explore P62399 
Go to UniProtKB:  P62399
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6f176Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
Explore P0AG55 
Go to UniProtKB:  P0AG55
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9g149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Explore P0A7R1 
Go to UniProtKB:  P0A7R1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10h131Escherichia coliMutation(s): 0 
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Explore P0A7J3 
Go to UniProtKB:  P0A7J3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11i141Escherichia coliMutation(s): 0 
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Explore P0A7J7 
Go to UniProtKB:  P0A7J7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13j142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
Explore P0AA10 
Go to UniProtKB:  P0AA10
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15l143Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
Explore P02413 
Go to UniProtKB:  P02413
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17n120Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
Explore P0AG44 
Go to UniProtKB:  P0AG44
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18o116Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
Explore P0C018 
Go to UniProtKB:  P0C018
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19p114Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Explore P0A7K6 
Go to UniProtKB:  P0A7K6
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20q117Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Explore P0A7L3 
Go to UniProtKB:  P0A7L3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21r103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
Explore P0AG48 
Go to UniProtKB:  P0AG48
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22s110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
Explore P61175 
Go to UniProtKB:  P61175
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23t93Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Explore P0ADZ0 
Go to UniProtKB:  P0ADZ0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24u102Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
Explore P60624 
Go to UniProtKB:  P60624
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25v94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
Explore P68919 
Go to UniProtKB:  P68919
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27w75Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Explore P0A7L8 
Go to UniProtKB:  P0A7L8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28x77Escherichia coliMutation(s): 0 
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Explore P0A7M2 
Go to UniProtKB:  P0A7M2
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29y63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
Go to UniProtKB:  P0A7M6
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30z58Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
Explore P0AG51 
Go to UniProtKB:  P0AG51
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31A70Escherichia coliMutation(s): 0 
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Explore P0A7M9 
Go to UniProtKB:  P0A7M9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32B56Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Explore P0A7N4 
Go to UniProtKB:  P0A7N4
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34D46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Explore P0A7P5 
Go to UniProtKB:  P0A7P5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35E64Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Explore P0A7Q1 
Go to UniProtKB:  P0A7Q1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2G225Escherichia coliMutation(s): 0 
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Explore P0A7V0 
Go to UniProtKB:  P0A7V0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3H206Escherichia coliMutation(s): 0 
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Explore P0A7V3 
Go to UniProtKB:  P0A7V3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4I205Escherichia coliMutation(s): 0 
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Explore P0A7V8 
Go to UniProtKB:  P0A7V8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5J157Escherichia coliMutation(s): 0 
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Explore P0A7W1 
Go to UniProtKB:  P0A7W1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6K100Escherichia coliMutation(s): 0 
Find proteins for P02358 (Escherichia coli (strain K12))
Explore P02358 
Go to UniProtKB:  P02358
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7L151Escherichia coliMutation(s): 0 
Find proteins for P02359 (Escherichia coli (strain K12))
Explore P02359 
Go to UniProtKB:  P02359
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8M129Escherichia coliMutation(s): 0 
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Explore P0A7W7 
Go to UniProtKB:  P0A7W7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9N127Escherichia coliMutation(s): 0 
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Explore P0A7X3 
Go to UniProtKB:  P0A7X3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10O98Escherichia coliMutation(s): 0 
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Explore P0A7R5 
Go to UniProtKB:  P0A7R5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11P116Escherichia coliMutation(s): 0 
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Explore P0A7R9 
Go to UniProtKB:  P0A7R9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12Q123Escherichia coliMutation(s): 0 
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Explore P0A7S3 
Go to UniProtKB:  P0A7S3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13R114Escherichia coliMutation(s): 0 
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Explore P0A7S9 
Go to UniProtKB:  P0A7S9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14S100Escherichia coliMutation(s): 0 
Find proteins for P0AG59 (Escherichia coli (strain K12))
Explore P0AG59 
Go to UniProtKB:  P0AG59
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15T88Escherichia coliMutation(s): 0 
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Explore P0ADZ4 
Go to UniProtKB:  P0ADZ4
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16U82Escherichia coliMutation(s): 0 
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Explore P0A7T3 
Go to UniProtKB:  P0A7T3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17V80Escherichia coliMutation(s): 0 
Find proteins for P0AG63 (Escherichia coli (strain K12))
Explore P0AG63 
Go to UniProtKB:  P0AG63
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18W65Escherichia coliMutation(s): 0 
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Explore P0A7T7 
Go to UniProtKB:  P0A7T7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19X79Escherichia coliMutation(s): 0 
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Explore P0A7U3 
Go to UniProtKB:  P0A7U3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20Y85Escherichia coliMutation(s): 0 
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Explore P0A7U7 
Go to UniProtKB:  P0A7U7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21Z65Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
Explore P68679 
Go to UniProtKB:  P68679
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1a223Escherichia coliMutation(s): 0 
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Explore P0A7L0 
Go to UniProtKB:  P0A7L0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14k122Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Explore P0ADY3 
Go to UniProtKB:  P0ADY3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36F38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Explore P0A7Q6 
Go to UniProtKB:  P0A7Q6
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4d201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
Explore P60723 
Go to UniProtKB:  P60723
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 51
MoleculeChainsLengthOrganism
16S ribosomal RNA31539Escherichia coli

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 52
MoleculeChainsLengthOrganism
23s-5s joint ribosomal RNA43031Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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