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: 3.7 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

  • 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.,From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
E
234Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplA
Find proteins for B7MIX0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
F
273Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplB
Find proteins for B7MCT2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
G
209Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplC
Find proteins for B7MCT5 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
H
201Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplD
Find proteins for B7MCT4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT4
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
I
179Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplE
Find proteins for B7MCS3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
J
177Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplF
Find proteins for B7MCS0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
K
149Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplI
Find proteins for B7MLK8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MLK8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
L
165Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplJ
Find proteins for B7MIX1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
M
142Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplK
Find proteins for B7MIW9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIW9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
N
142Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplM
Find proteins for B7MBZ2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBZ2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
O
123Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplN
Find proteins for B7MCS5 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
P
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
Q
136Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplP
Find proteins for B7MCS8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
R
127Escherichia coli O81 (strain ED1a)Mutation(s): 0 
Gene Names: rplQ
Find proteins for B7N179 (Escherichia coli O81 (strain ED1a))
Go to UniProtKB:  B7N179
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
S
117Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplR
Find proteins for B7MCR9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR9
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
T
115Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplS
Find proteins for B7MIU4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIU4
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
U
118Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplT
Find proteins for B7MAS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAS6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
V
103Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplU
Find proteins for B7MBV5 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBV5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
W
110Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplV
Find proteins for B7MCT0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
X
100Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rplW
Find proteins for B7MCT3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
Y
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
Z
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AA
85Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmA
Find proteins for B7MBV4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBV4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BA
78Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmB
Find proteins for B7MFJ8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MFJ8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
CA
63Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmC
Find proteins for B7MCS7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS7
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
DA
59Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmD
Find proteins for B7MCR7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR7
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
EA
70Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmE
Find proteins for B7MI68 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MI68
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
FA
57Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmF
Find proteins for B7MJ76 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MJ76
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
GA
55Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmG
Find proteins for B7MFJ7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MFJ7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
HA
46Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmH
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MGC4
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
IA
65Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmI
Find proteins for B7MAS7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAS7
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
JA
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 1
MA
362Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: prfA
Find proteins for B7MKB3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MKB3
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
OA
241Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsB
Find proteins for B7MBF0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBF0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
PA
233Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsC
Find proteins for B7MCS9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS9
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
QA
206Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsD
Find proteins for B7MCR2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR2
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
RA
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
SA
131Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
TA
156Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsG
Find proteins for B7MCV6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCV6
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
UA
130Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsH
Find proteins for B7MCS1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS1
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
VA
130Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsI
Find proteins for B7MBZ1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MBZ1
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
WA
103Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for B7MCT6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT6
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
XA
129Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsK
Find proteins for B7MCR3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCR3
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
YA
124Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsL
Find proteins for B7MCV7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCV7
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
ZA
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AB
102Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsN
Find proteins for B7MCS2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS2
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BB
89Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsO
Find proteins for B7MB86 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MB86
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
CB
82Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsP
Find proteins for B7MIU7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIU7
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
DB
84Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for B7MCS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCS6
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
EB
75Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsR
Find proteins for B7MLK7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MLK7
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
FB
92Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsS
Find proteins for B7MCT1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MCT1
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
GB
87Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsT
Find proteins for B7MAE3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAE3
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
HB
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1539Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNAB2903Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNAC120Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
tRNA(fMet)D,LA77Escherichia coli
Entity ID: 37
MoleculeChainsLengthOrganism
mRNAKA27synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references, Experimental preparation
  • Version 1.2: 2018-08-22
    Type: Data collection, Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence