5MDY

Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Translational termination without a stop codon.

James, N.R.Brown, A.Gordiyenko, Y.Ramakrishnan, V.

(2016) Science 354: 1437-1440

  • DOI: 10.1126/science.aai9127
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine str ...

    Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.


    Organizational Affiliation

    Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
7
378Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0142prfB
Find proteins for Q5SM01 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
H
165Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
Find proteins for P0A7J3 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
g
241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
i
206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
l
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
m
130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
n
130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
o
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
Find proteins for P0A7R5 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
p
129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
u
82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
x
92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
y
87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
a
70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
h
233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
j
167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
k
135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
q
124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
r
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
Find proteins for P0A7S9 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
s
101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
t
89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
v
84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
w
75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
z
71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Alternative ribosome-rescue factor A
6
61Escherichia coli K-12Mutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
Find proteins for P36675 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli K-12

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Entity ID: 5
MoleculeChainsLengthOrganism
fMet-NH-tRNA(fMet)578Escherichia coli

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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA12904Escherichia coli K-12

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Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21534Escherichia coli K-12
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Entity ID: 4
MoleculeChainsLengthOrganism
mRNA418Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download CCD File 
5
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

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a, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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1, 2, 3, 5, b, f, i
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
5L-PEPTIDE LINKINGC6 H11 N O3 SMET
0TD
Query on 0TD
qL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations, Experimental preparation
  • Version 2.0: 2018-10-17
    Changes: Data collection, Polymer sequence, Refinement description
  • Version 2.1: 2019-12-11
    Changes: Advisory, Derived calculations, Other