6VWM

70S ribosome bound to HIV frameshifting stem-loop (FSS) and P-site tRNA (non-rotated conformation, Structure I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
B
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
C
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
D
179Escherichia coliMutation(s): 0 
Find proteins for D7Z9G7 (Escherichia coli MS 69-1)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
H
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
K
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
L
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
T
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
t
71Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
I
123Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
J
144Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
M
117Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
N
115Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
O
118Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
P
103Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
Q
110Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
R
100Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
S
104Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
U
85Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
V
78Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
W
63Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
X
59Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Y
57Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
Z
55Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
AA
46Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
AB
65Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
A
273Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
AC
38Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
a
241Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
b
233Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
c
206Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
d
167Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
e
135Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
f
179Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
g
130Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
h
130Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
i
103Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
j
129Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
k
124Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
l
118Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
m
101Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
n
89Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
o
82Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
p
84Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
q
75Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
r
92Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
s
87Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
E
177Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli

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Entity ID: 2
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
1, 2, A, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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