6DNC

E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of premature translation termination on a sense codon.

Svidritskiy, E.Demo, G.Korostelev, A.A.

(2018) J Biol Chem 293: 12472-12479

  • DOI: 10.1074/jbc.AW118.003232
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nev ...

    Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nevertheless, some sense codons are prone to triggering premature termination, but the structural basis for this is unclear. To investigate premature termination, we determined a cryo-EM structure of the Escherichia coli 70S ribosome bound with RF1 in response to a UAU (Tyr) sense codon. The structure reveals that RF1 recognizes a UAU codon similarly to a UAG stop codon, suggesting that sense codons induce premature termination because they structurally mimic a stop codon. Hydrophobic interaction between the nucleobase of U3 (the third position of the UAU codon) and conserved Ile-196 in RF1 is important for misreading the UAU codon. Analyses of RNA binding in ribonucleoprotein complexes or by amino acids reveal that Ile-U packing is a frequent protein-RNA-binding motif with key functional implications. We discuss parallels with eukaryotic translation termination by the release factor eRF1.


    Organizational Affiliation

    From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605 andrei.korostelev@umassmed.edu.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
E
234Escherichia coliMutation(s): 0 
Find proteins for B7MIX0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
F
273Escherichia coliMutation(s): 0 
Find proteins for B7MCT2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
H
201Escherichia coliMutation(s): 0 
Find proteins for B7MCT4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
I
179Escherichia coliMutation(s): 0 
Find proteins for B7MCS3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
J
177Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
L
165Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
M
142Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
N
142Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
O
123Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
P
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
R
127Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
S
117Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
T
115Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
U
118Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
V
103Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
W
110Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
X
100Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
Y
104Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
Z
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AA
85Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BA
78Escherichia coliMutation(s): 0 
Find proteins for B7MFJ8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
CA
63Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
DA
59Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
EA
70Escherichia coliMutation(s): 0 
Find proteins for B7MI68 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
FA
57Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
GA
55Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
HA
46Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
IA
65Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
JA
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 1
MA
362Escherichia coliMutation(s): 0 
Gene Names: prfAECS88_1279
Find proteins for B7MKB3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
OA
241Escherichia coliMutation(s): 0 
Find proteins for B7MBF0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
PA
233Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
QA
206Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
RA
167Escherichia coliMutation(s): 0 
Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
SA
131Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
TA
156Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
UA
130Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
VA
130Escherichia coliMutation(s): 0 
Find proteins for B7MBZ1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
WA
103Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
XA
129Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
YA
124Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
ZA
118Escherichia coliMutation(s): 0 
Find proteins for P0A7S9 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AB
102Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BB
89Escherichia coliMutation(s): 0 
Find proteins for B7MB86 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
CB
82Escherichia coliMutation(s): 0 
Find proteins for B7MIU7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
DB
84Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
EB
75Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
GB
87Escherichia coliMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
HB
71Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
K
149Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
Q
136Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
FB
92Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
G
209Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1539Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNAB2903Escherichia coli

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Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNAC120Escherichia coli

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Entity ID: 4
MoleculeChainsLengthOrganism
tRNA(fMet)D, LA77Escherichia coli

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Entity ID: 37
MoleculeChainsLengthOrganism
mRNAKA27synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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 StatesGM107465

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.2: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence