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


This is version 1.0 of the entry. See complete history


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: https://doi.org/10.7554/eLife.55799
  • Primary Citation of Related Structures:  
    6VWL, 6VWM, 6VWN

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2273Escherichia coliMutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L3209Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4201Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5179Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6177Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9149Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13142Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth I]123Escherichia coliMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L15I [auth J]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16J [auth K]136Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L17K [auth L]127Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L18L [auth M]117Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19M [auth N]115Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20N [auth O]118Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21O [auth P]103Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L22P [auth Q]110Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Q [auth R]100Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24R [auth S]104Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25S [auth T]94Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27T [auth U]85Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28U [auth V]78Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29V [auth W]63Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30W [auth X]59Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32X [auth Y]57Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L33Y [auth Z]55Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Z [auth AA]46Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AA [auth AB]65Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth AC]38Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2FA [auth a]241Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3GA [auth b]233Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4HA [auth c]206Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5IA [auth d]167Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6JA [auth e]135Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7KA [auth f]179Escherichia coliMutation(s): 0 
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Entity ID: 38
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30S ribosomal protein S8LA [auth g]130Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9MA [auth h]130Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10NA [auth i]103Escherichia coliMutation(s): 0 
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Entity ID: 41
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30S ribosomal protein S11OA [auth j]129Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12PA [auth k]124Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13QA [auth l]118Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14RA [auth m]101Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth n]89Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth o]82Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth p]84Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth q]75Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19WA [auth r]92Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth s]87Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21YA [auth t]71Escherichia coliMutation(s): 0 
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UniProt GroupP68679
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Entity ID: 28
MoleculeChains LengthOrganismImage
5S ribosomal RNABA [auth 3]120Escherichia coli
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Entity ID: 29
MoleculeChains LengthOrganismImage
tRNAPheCA [auth 5]76Escherichia coli
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Entity ID: 31
MoleculeChains LengthOrganismImage
23S ribosomal RNAEA [auth 2]2,903Escherichia coli
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Entity ID: 52
MoleculeChains LengthOrganismImage
16S ribosomal RNAZA [auth 1]1,540Escherichia coli
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Entity ID: 53
MoleculeChains LengthOrganismImage
HIV frameshift stimulating sequence mRNAAB [auth 4]93Human immunodeficiency virus 1
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 2]
BB [auth A]
BC [auth 2]
CB [auth B]
CC [auth 2]
AC [auth 2],
BB [auth A],
BC [auth 2],
CB [auth B],
CC [auth 2],
DB [auth 3],
DC [auth 2],
EB [auth 3],
EC [auth 2],
FB [auth 3],
FC [auth 2],
GB [auth 3],
GC [auth 2],
HB [auth 3],
HC [auth 2],
IB [auth 2],
IC [auth 1],
JB [auth 2],
KB [auth 2],
LB [auth 2],
MB [auth 2],
NB [auth 2],
OB [auth 2],
PB [auth 2],
QB [auth 2],
RB [auth 2],
SB [auth 2],
TB [auth 2],
UB [auth 2],
VB [auth 2],
WB [auth 2],
XB [auth 2],
YB [auth 2],
ZB [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX1.17

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 StatesR01GM099719
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

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