6VWL

70S ribosome bound to HIV frameshifting stem-loop (FSS) and P/E tRNA (rotated conformation)


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report



Literature

mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.

Bao, C.Loerch, S.Ling, C.Korostelev, A.A.Grigorieff, N.Ermolenko, D.N.

(2020) Elife 9

  • DOI: 10.7554/eLife.55799
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemic ...

    Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Förster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape the ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.


    Organizational Affiliation

    Department of Biochemistry and Biophysics at School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2A273Escherichia coliMutation(s): 0 
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50S ribosomal protein L4C201Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5D179Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6E177Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9F149Escherichia coliMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L13G142Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14I123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15J144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16K136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17L127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18M117Escherichia coliMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L19N115Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L20O118Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L21P103Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L22Q110Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L23R100Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24S104Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L25T94Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27U85Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L28V78Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29W63Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30X59Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32Y57Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33Z55Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34AA46Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35AB65Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36AC38Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2a241Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3b233Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4c206Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5d167Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6e135Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7f179Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8g130Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9h130Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10i103Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11j129Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12k124Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13l118Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14m101Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15n89Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16o82Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17p84Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18q75Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19r92Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20s87Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21t71Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3B209Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsLengthOrganism
tRNAPhe576Escherichia coli

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Entity ID: 31
MoleculeChainsLengthOrganism
23S ribosomal RNA22903Escherichia coli

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Entity ID: 52
MoleculeChainsLengthOrganism
16S ribosomal RNA11540Escherichia coli

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Entity ID: 53
MoleculeChainsLengthOrganism
HIV frameshift stimulating sequence mRNA493Human immunodeficiency virus 1

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Entity ID: 28
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
1, 2, 3, A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 StatesR01GM099719
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2020-06-03
    Type: Initial release