6Q98

Structure of tmRNA SmpB bound in P site of E. coli 70S ribosome

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-12-17 Released: 2019-02-27 
  • Deposition Author(s): Rae, C.D.
  • Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

How a circularized tmRNA moves through the ribosome.

Rae, C.D.Gordiyenko, Y.Ramakrishnan, V.

(2019) Science 363: 740-744

  • DOI: 10.1126/science.aav9370
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of ...

    During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK. ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SsrA-binding protein
5
160Escherichia coliMutation(s): 0 
Gene Names: smpBHMPREF1589_02201
Find proteins for U9Y9P1 (Escherichia coli 113290)
Go to UniProtKB:  U9Y9P1

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Nascent peptide
6
22Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
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: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
H
165Escherichia coliMutation(s): 0 
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coliMutation(s): 0 
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 18
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: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 21
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: 22
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: 23
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: 24
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: 25
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: 26
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: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
85Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 28
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: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6

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Entity ID: 30
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: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
a
70Escherichia coliMutation(s): 0 
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
65Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
g
241Escherichia coliMutation(s): 0 
Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 38
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: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
i
206Escherichia coliMutation(s): 0 
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 40
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 S8
m
130Escherichia coliMutation(s): 0 
Find proteins for P0A7W7 (Escherichia coli (strain K12))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
n
130Escherichia coliMutation(s): 0 
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
o
103Escherichia coliMutation(s): 0 
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Entity ID: 46
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: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
q
124Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 48
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: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
s
101Escherichia coliMutation(s): 0 
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
t
89Escherichia coliMutation(s): 0 
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
u
82Escherichia coliMutation(s): 0 
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
v
84Escherichia coliMutation(s): 0 
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
x
92Escherichia coliMutation(s): 0 
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 56
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: 10
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: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
55Escherichia coliMutation(s): 0 
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 41
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: 42
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: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
w
75Escherichia coliMutation(s): 0 
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
y
87Escherichia coliMutation(s): 0 
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 7
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: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
179Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399

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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA12904Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21535Escherichia coli

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Entity ID: 57
MoleculeChainsLengthOrganism
transfer-messenger RNA (tmRNA)4363Escherichia coli

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Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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, 4, B, C, L, N, U, f, i, r
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
qL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-12-17 
  • Released Date: 2019-02-27 
  • Deposition Author(s): Rae, C.D.

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

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release