7AC7

Structure of accomodated trans-translation complex on E. Coli stalled ribosome.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 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

Structures of tmRNA and SmpB as they transit through the ribosome.

Guyomar, C., D'Urso, G., Chat, S., Giudice, E., Gillet, R.

(2021) Nat Commun 12: 4909-4909

  • DOI: https://doi.org/10.1038/s41467-021-24881-4
  • Primary Citation of Related Structures:  
    7ABZ, 7AC7, 7ACJ, 7ACR

  • PubMed Abstract: 

    In bacteria, trans-translation is the main rescue system, freeing ribosomes stalled on defective messenger RNAs. This mechanism is driven by small protein B (SmpB) and transfer-messenger RNA (tmRNA), a hybrid RNA known to have both a tRNA-like and an mRNA-like domain. Here we present four cryo-EM structures of the ribosome during trans-translation at resolutions from 3.0 to 3.4 Å. These include the high-resolution structure of the whole pre-accommodated state, as well as structures of the accommodated state, the translocated state, and a translocation intermediate. Together, they shed light on the movements of the tmRNA-SmpB complex in the ribosome, from its delivery by the elongation factor EF-Tu to its passage through the ribosomal A and P sites after the opening of the B1 bridges. Additionally, we describe the interactions between the tmRNA-SmpB complex and the ribosome. These explain why the process does not interfere with canonical translation.

    • Organizational Affiliation: 

    Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SsrA-binding proteinE [auth 5]147Escherichia coli K-12Mutation(s): 0 
Gene Names: smpB, smqB, b2620, JW2601
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27H [auth A]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth B]271Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3J [auth C]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4K [auth D]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5L [auth E]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6M [auth F]175Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9N [auth G]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10O [auth H]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13P [auth J]141Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14Q [auth K]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15R [auth L]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16S [auth M]136Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17T [auth N]119Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18U [auth O]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19V [auth P]114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20W [auth Q]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21X [auth R]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Y [auth S]109Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Z [auth T]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24AA [auth U]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25BA [auth V]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent peptideCA [auth W]2Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28DA [auth X]77Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29EA [auth Y]58Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30FA [auth Z]56Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31GA [auth a]66Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32HA [auth b]54Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L33IA [auth c]52Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L34JA [auth d]46Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L35KA [auth e]64Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36LA [auth f]37Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2MA [auth g]225Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S3NA [auth h]208Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S4OA [auth i]205Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S5PA [auth j]156Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S6QA [auth k]104Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7RA [auth l]151Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8SA [auth m]129Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9TA [auth n]126Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10UA [auth o]99Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11VA [auth p]117Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12WA [auth q]123Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13XA [auth r]115Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14YA [auth s]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15ZA [auth t]87Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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UniProt GroupP0ADZ4
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16AB [auth u]81Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17BB [auth v]80Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18CB [auth w]65Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19DB [auth x]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20EB [auth y]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21FB [auth z]70Escherichia coli K-12Mutation(s): 0 
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Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 1]2,903Escherichia coli K-12
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Entity ID: 2
MoleculeChains LengthOrganismImage
16S ribosomal RNAB [auth 2]1,540Escherichia coli K-12
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 3]120Escherichia coli K-12
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Entity ID: 4
MoleculeChains LengthOrganismImage
transfer-messenger RNA (tmRNA)D [auth 4]363Escherichia coli
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Entity ID: 6
MoleculeChains LengthOrganismImage
tRNA-PheF [auth 7]76Escherichia coli
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Entity ID: 7
MoleculeChains LengthOrganismImage
mRNAG [auth 8]15Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
DS [auth a],
GS [auth f]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth 1]
AD [auth 1]
AE [auth 1]
AF [auth 1]
AG [auth 1]
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
AH [auth 1],
AI [auth 1],
AJ [auth 1],
AK [auth 1],
AL [auth 1],
AM [auth 1],
AN [auth 2],
AO [auth 2],
AP [auth 2],
AQ [auth 2],
AR [auth 2],
AS [auth Q],
BC [auth 1],
BD [auth 1],
BE [auth 1],
BF [auth 1],
BG [auth 1],
BH [auth 1],
BI [auth 1],
BJ [auth 1],
BK [auth 1],
BL [auth 1],
BM [auth 1],
BN [auth 2],
BO [auth 2],
BP [auth 2],
BQ [auth 2],
BR [auth 2],
BS [auth Q],
CC [auth 1],
CD [auth 1],
CE [auth 1],
CF [auth 1],
CG [auth 1],
CH [auth 1],
CI [auth 1],
CJ [auth 1],
CK [auth 1],
CL [auth 1],
CM [auth 1],
CN [auth 2],
CO [auth 2],
CP [auth 2],
CQ [auth 2],
CR [auth 2],
CS [auth Z],
DC [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth 1],
DG [auth 1],
DH [auth 1],
DI [auth 1],
DJ [auth 1],
DK [auth 1],
DL [auth 1],
DM [auth 1],
DN [auth 2],
DO [auth 2],
DP [auth 2],
DQ [auth 2],
DR [auth 2],
EC [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth 1],
EG [auth 1],
EH [auth 1],
EI [auth 1],
EJ [auth 1],
EK [auth 1],
EL [auth 1],
EM [auth 1],
EN [auth 2],
EO [auth 2],
EP [auth 2],
EQ [auth 2],
ER [auth 2],
ES [auth b],
FC [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth 1],
FG [auth 1],
FH [auth 1],
FI [auth 1],
FJ [auth 1],
FK [auth 1],
FL [auth 1],
FM [auth 1],
FN [auth 2],
FO [auth 2],
FP [auth 2],
FQ [auth 2],
FR [auth 2],
FS [auth b],
GB [auth 1],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 1],
GH [auth 1],
GI [auth 1],
GJ [auth 1],
GK [auth 1],
GL [auth 1],
GM [auth 1],
GN [auth 2],
GO [auth 2],
GP [auth 2],
GQ [auth 2],
GR [auth 2],
HB [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 1],
HH [auth 1],
HI [auth 1],
HJ [auth 1],
HK [auth 1],
HL [auth 1],
HM [auth 1],
HN [auth 2],
HO [auth 2],
HP [auth 2],
HQ [auth 2],
HR [auth 2],
IB [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 1],
IH [auth 1],
II [auth 1],
IJ [auth 1],
IK [auth 1],
IL [auth 1],
IM [auth 1],
IN [auth 2],
IO [auth 2],
IP [auth 2],
IQ [auth 2],
IR [auth 2],
JB [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 1],
JH [auth 1],
JI [auth 1],
JJ [auth 1],
JK [auth 1],
JL [auth 1],
JM [auth 1],
JN [auth 2],
JO [auth 2],
JP [auth 2],
JQ [auth 2],
JR [auth 2],
KB [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 1],
KH [auth 1],
KI [auth 1],
KJ [auth 1],
KK [auth 1],
KL [auth 1],
KM [auth 1],
KN [auth 2],
KO [auth 2],
KP [auth 2],
KQ [auth 2],
KR [auth 2],
LB [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 1],
LH [auth 1],
LI [auth 1],
LJ [auth 1],
LK [auth 1],
LL [auth 1],
LM [auth 1],
LN [auth 2],
LO [auth 2],
LP [auth 2],
LQ [auth 2],
LR [auth 3],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 1],
MH [auth 1],
MI [auth 1],
MJ [auth 1],
MK [auth 1],
ML [auth 1],
MM [auth 1],
MN [auth 2],
MO [auth 2],
MP [auth 2],
MQ [auth 2],
MR [auth 3],
NB [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 1],
NH [auth 1],
NI [auth 1],
NJ [auth 1],
NK [auth 1],
NL [auth 1],
NM [auth 1],
NN [auth 2],
NO [auth 2],
NP [auth 2],
NQ [auth 2],
NR [auth 3],
OB [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 1],
OH [auth 1],
OI [auth 1],
OJ [auth 1],
OK [auth 1],
OL [auth 1],
OM [auth 1],
ON [auth 2],
OO [auth 2],
OP [auth 2],
OQ [auth 2],
OR [auth 3],
PB [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth 1],
PF [auth 1],
PG [auth 1],
PH [auth 1],
PI [auth 1],
PJ [auth 1],
PK [auth 1],
PL [auth 1],
PM [auth 1],
PN [auth 2],
PO [auth 2],
PP [auth 2],
PQ [auth 2],
PR [auth 3],
QB [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth 1],
QF [auth 1],
QG [auth 1],
QH [auth 1],
QI [auth 1],
QJ [auth 1],
QK [auth 1],
QL [auth 1],
QM [auth 1],
QN [auth 2],
QO [auth 2],
QP [auth 2],
QQ [auth 2],
QR [auth 3],
RB [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 1],
RH [auth 1],
RI [auth 1],
RJ [auth 1],
RK [auth 1],
RL [auth 1],
RM [auth 1],
RN [auth 2],
RO [auth 2],
RP [auth 2],
RQ [auth 2],
RR [auth 3],
SB [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 1],
SH [auth 1],
SI [auth 1],
SJ [auth 1],
SK [auth 1],
SL [auth 1],
SM [auth 1],
SN [auth 2],
SO [auth 2],
SP [auth 2],
SQ [auth 2],
SR [auth 3],
TB [auth 1],
TC [auth 1],
TD [auth 1],
TE [auth 1],
TF [auth 1],
TG [auth 1],
TH [auth 1],
TI [auth 1],
TJ [auth 1],
TK [auth 1],
TL [auth 1],
TM [auth 1],
TN [auth 2],
TO [auth 2],
TP [auth 2],
TQ [auth 2],
TR [auth 3],
UB [auth 1],
UC [auth 1],
UD [auth 1],
UE [auth 1],
UF [auth 1],
UG [auth 1],
UH [auth 1],
UI [auth 1],
UJ [auth 1],
UK [auth 1],
UL [auth 1],
UM [auth 1],
UN [auth 2],
UO [auth 2],
UP [auth 2],
UQ [auth 2],
UR [auth 7],
VB [auth 1],
VC [auth 1],
VD [auth 1],
VE [auth 1],
VF [auth 1],
VG [auth 1],
VH [auth 1],
VI [auth 1],
VJ [auth 1],
VK [auth 1],
VL [auth 1],
VM [auth 1],
VN [auth 2],
VO [auth 2],
VP [auth 2],
VQ [auth 2],
VR [auth B],
WB [auth 1],
WC [auth 1],
WD [auth 1],
WE [auth 1],
WF [auth 1],
WG [auth 1],
WH [auth 1],
WI [auth 1],
WJ [auth 1],
WK [auth 1],
WL [auth 1],
WM [auth 1],
WN [auth 2],
WO [auth 2],
WP [auth 2],
WQ [auth 2],
WR [auth B],
XB [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth 1],
XF [auth 1],
XG [auth 1],
XH [auth 1],
XI [auth 1],
XJ [auth 1],
XK [auth 1],
XL [auth 1],
XM [auth 2],
XN [auth 2],
XO [auth 2],
XP [auth 2],
XQ [auth 2],
XR [auth C],
YB [auth 1],
YC [auth 1],
YD [auth 1],
YE [auth 1],
YF [auth 1],
YG [auth 1],
YH [auth 1],
YI [auth 1],
YJ [auth 1],
YK [auth 1],
YL [auth 1],
YM [auth 2],
YN [auth 2],
YO [auth 2],
YP [auth 2],
YQ [auth 2],
YR [auth D],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 1],
ZG [auth 1],
ZH [auth 1],
ZI [auth 1],
ZJ [auth 1],
ZK [auth 1],
ZL [auth 1],
ZM [auth 2],
ZN [auth 2],
ZO [auth 2],
ZP [auth 2],
ZQ [auth 2],
ZR [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
4D4
Query on 4D4		S [auth M]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
0TD
Query on 0TD		WA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
MODEL REFINEMENTCoot0.9
RECONSTRUCTIONRELION3.0.8

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceRIBOTARGET - 18-JAM2-0005-03
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05
European Union (EU)FranceErasmus+
French Ministry of Armed ForcesFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-04-24
    Changes: Data collection, Derived calculations, Refinement description