6Q9A

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

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

  • Deposited: 2018-12-17 Released: 2019-04-17 
  • Deposition Author(s): Rae, C.D.
  • Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

How a circularized tmRNA moves through the ribosome.

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

(2019) Science 363: 740-744

  • DOI: https://doi.org/10.1126/science.aav9370
  • Primary Citation of Related Structures:  
    6Q95, 6Q97, 6Q98, 6Q9A

  • 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 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.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent peptideD [auth 6]23Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2F [auth B]271Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3G [auth C]207Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4H [auth D]201Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5I [auth E]177Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6J [auth F]175Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9K [auth G]148Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10L [auth H]130Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11M [auth I]135Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13N [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L14O [auth K]123Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15P [auth L]143Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16Q [auth M]135Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L17R [auth N]119Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18S [auth O]115Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19T [auth P]113Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20U [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21V [auth R]102Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22W [auth S]109Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23X [auth T]94Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Y [auth U]101Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25Z [auth V]93Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AA [auth W]75Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BA [auth X]77Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CA [auth Y]62Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth Z]56Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31EA [auth a]66Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32FA [auth b]55Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33GA [auth c]51Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34HA [auth d]45Escherichia coliMutation(s): 0 
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Entity ID: 35
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50S ribosomal protein L35IA [auth e]64Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36JA [auth f]38Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2KA [auth g]225Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3LA [auth h]208Escherichia coliMutation(s): 0 
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Entity ID: 39
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30S ribosomal protein S4MA [auth i]205Escherichia coliMutation(s): 0 
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Entity ID: 40
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30S ribosomal protein S5NA [auth j]156Escherichia coliMutation(s): 0 
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Entity ID: 41
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30S ribosomal protein S6OA [auth k]104Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7PA [auth l]152Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8QA [auth m]129Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9RA [auth n]127Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10SA [auth o]99Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11TA [auth p]116Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12UA [auth q]122Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13VA [auth r]116Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14WA [auth s]100Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15XA [auth t]87Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16YA [auth u]82Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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UniProt GroupP0A7T3
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17ZA [auth v]80Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18AB [auth w]66Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19BB [auth x]83Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20CB [auth y]85Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21DB [auth z]70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
SsrA-binding proteinEB [auth 5]118Escherichia coliMutation(s): 0 
Gene Names: smpB, ERS085411_03441
UniProt
Find proteins for P0A832 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 1]2,903Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
16S ribosomal RNAB [auth 2]1,534Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 3]120Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
P-site tRNAE [auth 7]76Escherichia coli
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Entity ID: 58
MoleculeChains LengthOrganismImage
tmRNAFB [auth 4]363Escherichia 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 
AS [auth f],
XR [auth a]		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],
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 i],
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 s],
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],
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],
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 3],
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 3],
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 2],
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 2],
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 2],
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 2],
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 2],
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 2],
RN [auth 2],
RO [auth 2],
RP [auth 2],
RQ [auth 2],
RR [auth 7],
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 2],
SN [auth 2],
SO [auth 2],
SP [auth 2],
SQ [auth 2],
SR [auth 7],
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 2],
TN [auth 2],
TO [auth 2],
TP [auth 2],
TQ [auth 2],
TR [auth 7],
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 2],
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 2],
VN [auth 2],
VO [auth 2],
VP [auth 2],
VQ [auth 2],
VR [auth O],
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 2],
WN [auth 2],
WO [auth 2],
WP [auth 2],
WQ [auth 2],
WR [auth Q],
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],
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 b],
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 f]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0TD
Query on 0TD		UA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



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

Deposition Data

  • Released Date: 2019-04-17 
    • Deposition Author(s): Rae, C.D.
Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description