6HRM

E. coli 70S d2d8 stapled ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 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

Controlling orthogonal ribosome subunit interactions enables evolution of new function.

Schmied, W.H.Tnimov, Z.Uttamapinant, C.Rae, C.D.Fried, S.D.Chin, J.W.

(2018) Nature 564: 444-448

  • DOI: 10.1038/s41586-018-0773-z
  • Primary Citation of Related Structures:  
    6HRM

  • PubMed Abstract: 
  • Orthogonal ribosomes are unnatural ribosomes that are directed towards orthogonal messenger RNAs in Escherichia coli, through an altered version of the 16S ribosomal RNA of the small subunit 1 . Directed evolution of orthogonal ribosomes h ...

    Orthogonal ribosomes are unnatural ribosomes that are directed towards orthogonal messenger RNAs in Escherichia coli, through an altered version of the 16S ribosomal RNA of the small subunit 1 . Directed evolution of orthogonal ribosomes has provided access to new ribosomal function, and the evolved orthogonal ribosomes have enabled the encoding of multiple non-canonical amino acids into proteins 2-4 . The original orthogonal ribosomes shared the pool of 23S ribosomal RNAs, contained in the large subunit, with endogenous ribosomes. Selectively directing a new 23S rRNA to an orthogonal mRNA, by controlling the association between the orthogonal 16S rRNAs and 23S rRNAs, would enable the evolution of new function in the large subunit. Previous work covalently linked orthogonal 16S rRNA and a circularly permuted 23S rRNA to create orthogonal ribosomes with low activity 5,6 ; however, the linked subunits in these ribosomes do not associate specifically with each other, and mediate translation by associating with endogenous subunits. Here we discover engineered orthogonal 'stapled' ribosomes (with subunits linked through an optimized RNA staple) with activities comparable to that of the parent orthogonal ribosome; they minimize association with endogenous subunits and mediate translation of orthogonal mRNAs through the association of stapled subunits. We evolve cells with genomically encoded stapled ribosomes as the sole ribosomes, which support cellular growth at similar rates to natural ribosomes. Moreover, we visualize the engineered stapled ribosome structure by cryo-electron microscopy at 3.0 Å, revealing how the staple links the subunits and controls their association. We demonstrate the utility of controlling subunit association by evolving orthogonal stapled ribosomes which efficiently polymerize a sequence of monomers that the natural ribosome is intrinsically unable to translate. Our work provides a foundation for evolving the rRNA of the entire orthogonal ribosome for the encoded cellular synthesis of non-canonical biological polymers 7 .


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. chin@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 3
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50S ribosomal protein L2B271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3C209Escherichia coliMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L4D201Escherichia coliMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L5E177Escherichia coliMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L6F175Escherichia coliMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L9G149Escherichia coliMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L10H130Escherichia coliMutation(s): 0 
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50S ribosomal protein L11I135Escherichia coliMutation(s): 0 
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50S ribosomal protein L13J142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14K123Escherichia coliMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L15L144Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L16M136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17N119Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L18O116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19P114Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L20Q117Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L21R103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22S110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23T94Escherichia coliMutation(s): 0 
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50S ribosomal protein L24U103Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L25V94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W76Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L28X77Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L29Y62Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L30Z58Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L31a66Escherichia coliMutation(s): 0 
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50S ribosomal protein L32b56Escherichia coliMutation(s): 0 
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50S ribosomal protein L33c52Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L34d46Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L35e64Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L36f38Escherichia coliMutation(s): 0 
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Entity ID: 34
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30S ribosomal protein S2g225Escherichia coliMutation(s): 0 
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Entity ID: 35
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30S ribosomal protein S3h208Escherichia coliMutation(s): 0 
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Entity ID: 36
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30S ribosomal protein S4i205Escherichia coliMutation(s): 0 
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Entity ID: 37
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30S ribosomal protein S5j156Escherichia coliMutation(s): 0 
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Entity ID: 38
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30S ribosomal protein S6k104Escherichia coliMutation(s): 0 
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Entity ID: 39
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30S ribosomal protein S7l151Escherichia coliMutation(s): 0 
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Entity ID: 40
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30S ribosomal protein S8m129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9n127Escherichia coliMutation(s): 0 
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Entity ID: 42
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30S ribosomal protein S10o99Escherichia coliMutation(s): 0 
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Entity ID: 43
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30S ribosomal protein S11p117Escherichia coliMutation(s): 0 
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Entity ID: 44
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30S ribosomal protein S12q123Escherichia coliMutation(s): 0 
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Entity ID: 45
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30S ribosomal protein S13r116Escherichia coliMutation(s): 0 
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Entity ID: 46
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30S ribosomal protein S14s100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15t88Escherichia coliMutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S16u82Escherichia coliMutation(s): 0 
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Entity ID: 49
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30S ribosomal protein S17v80Escherichia coliMutation(s): 0 
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Entity ID: 50
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30S ribosomal protein S18w66Escherichia coliMutation(s): 0 
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Entity ID: 51
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30S ribosomal protein S19x83Escherichia coliMutation(s): 0 
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Entity ID: 52
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30S ribosomal protein S20y86Escherichia coliMutation(s): 0 
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Entity ID: 53
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30S ribosomal protein S21z70Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA14458Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNA3120Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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a, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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1, 3, N, P, Q, U, b, i
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
qL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105181009
Medical Research Council (United Kingdom)United KingdomMC_UP_A024_1008
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M000842/1
European Research CouncilBelgiumERC Advanced Grant (SGCR)

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-02
    Changes: Data collection, Database references