5H5U

Mechanistic insights into the alternative translation termination by ArfA and RF2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic insights into the alternative translation termination by ArfA and RF2

Ma, C.Kurita, D.Li, N.Chen, Y.Himeno, H.Gao, N.

(2017) Nature 541: 550-553

  • DOI: 10.1038/nature20822

  • PubMed Abstract: 
  • During cellular translation of messenger RNAs by ribosomes, the translation apparatus sometimes pauses or stalls at the elongation and termination steps. With the exception of programmed stalling, which is usually used by cells for regulatory purpose ...

    During cellular translation of messenger RNAs by ribosomes, the translation apparatus sometimes pauses or stalls at the elongation and termination steps. With the exception of programmed stalling, which is usually used by cells for regulatory purposes, ribosomes stalled on mRNAs need to be terminated and recycled to maintain adequate translation capacity. Much ribosome stalling originates in aberrant mRNAs that lack a stop codon. Transcriptional errors, misprocessing of primary transcripts, and undesired mRNA cleavage all contribute to the formation of non-stop mRNAs. Ribosomes stalled at the 3' end of non-stop mRNAs do not undergo normal termination owing to the lack of specific stop-codon recognition by canonical peptide release factors at the A-site decoding centre. In bacteria, the transfer-messenger RNA (tmRNA)-SmpB-mediated trans-translation rescue system reroutes stalled ribosomes to the normal elongation cycle and translation termination. Two additional rescue systems, ArfA-RF2 (refs 13, 14, 15, 16) and ArfB (formerly known as YaeJ), are also present in many bacterial species, but their mechanisms are not fully understood. Here, using cryo-electron microscopy, we characterize the structure of the Escherichia coli 70S ribosome bound with ArfA, the release factor RF2, a short non-stop mRNA and a cognate P-site tRNA. The C-terminal loop of ArfA occupies the mRNA entry channel on the 30S subunit, whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2. Despite the distinct conformation of RF2, its conserved catalytic GGQ motif is precisely positioned next to the CCA-end of the P-site tRNA. These data illustrate a stop-codon surrogate mechanism for ArfA in facilitating the termination of non-stop ribosomal complexes by RF2.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
1
86Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
2
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Alternative ribosome-rescue factor A
3
72Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: arfA (yhdL)
Find proteins for P36675 (Escherichia coli (strain K12))
Go to UniProtKB:  P36675
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
4
365Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: prfB (supK)
Find proteins for P07012 (Escherichia coli (strain K12))
Go to UniProtKB:  P07012
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
272Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
I
164Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
J
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
a
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
i
240Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
j
232Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
k
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
l
166Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
m
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
n
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
o
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
p
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
q
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
r
128Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
s
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
t
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
u
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
v
88Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
w
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
x
83Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
y
74Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
z
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 5
MoleculeChainsLengthOrganism
P-site tRNA576Escherichia coli
Entity ID: 6
MoleculeChainsLengthOrganism
mRNA76Escherichia coli
Entity ID: 7
MoleculeChainsLengthOrganism
23S rRNAA2903Escherichia coli K-12
Entity ID: 8
MoleculeChainsLengthOrganism
5S Ribosomal RNAB120Escherichia coli K-12
Entity ID: 39
MoleculeChainsLengthOrganism
16S rRNAh1534Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-08
    Type: Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Other, Refinement description