5MDW

Structure of ArfA(A18T) and RF2 bound to the 70S ribosome (pre-accommodated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 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: 6
MoleculeChainsSequence LengthOrganismDetails
Alternative ribosome-rescue factor A
6
61Escherichia coliMutation(s): 1 
Gene Names: arfAyhdLb4550JW3253
Find proteins for P36675 (Escherichia coli (strain K12))
Go to UniProtKB:  P36675
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
7
365Escherichia coliMutation(s): 0 
Gene Names: prfBsupKb2891JW5847
Find proteins for P07012 (Escherichia coli (strain K12))
Go to UniProtKB:  P07012
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
273Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
179Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
177Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 13
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: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
H
165Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
118Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
104Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
85Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
78Escherichia coliMutation(s): 0 
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
59Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
a
70Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
55Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
65Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
h
233Escherichia coliMutation(s): 0 
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
i
206Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
j
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
k
135Escherichia coliMutation(s): 0 
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
l
179Escherichia coliMutation(s): 0 
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
m
130Escherichia coliMutation(s): 0 
Find proteins for P0A7W7 (Escherichia coli (strain K12))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
n
130Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
o
103Escherichia coliMutation(s): 0 
Find proteins for P0A7R5 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
q
124Escherichia coliMutation(s): 0 
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
r
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
s
101Escherichia coliMutation(s): 0 
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
t
89Escherichia coliMutation(s): 0 
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
u
82Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
v
84Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
w
75Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
x
92Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
y
87Escherichia coliMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
z
71Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
g
241Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
p
129Escherichia coliMutation(s): 0 
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA12904Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21534Escherichia coli

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Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli
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Entity ID: 4
MoleculeChainsLengthOrganism
mRNA418Escherichia coli

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

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

Download CCD File 
1, 2, 3, 5, b, i
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
5L-PEPTIDE LINKINGC6 H11 N O3 SMET
MEQ
Query on MEQ
7L-PEPTIDE LINKINGC6 H12 N2 O3GLN
0TD
Query on 0TD
qL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2016-12-14
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 2.0: 2018-10-17
    Changes: Data collection, Polymer sequence, Refinement description
  • Version 2.1: 2019-12-11
    Changes: Advisory, Derived calculations, Other