6Q97

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

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

  • Deposited: 2018-12-17 Released: 2019-03-13 
  • Deposition Author(s): Rae, C.D.
  • Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 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 ...

    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.



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Entity ID: 4
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SsrA-binding proteinD [auth 5]145Escherichia coliMutation(s): 0 
Gene Names: smpBsmqBb2620JW2601
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Entity ID: 5
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Nascent peptideE [auth 6]28Escherichia coliMutation(s): 0 
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50S ribosomal protein L2H [auth B]270Escherichia coliMutation(s): 0 
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50S ribosomal protein L3I [auth C]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4J [auth D]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5K [auth E]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L29EA [auth Y]58Escherichia coliMutation(s): 0 
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50S ribosomal protein L36LA [auth f]37Escherichia coliMutation(s): 0 
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30S ribosomal protein S2MA [auth g]225Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18CB [auth w]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19DB [auth x]82Escherichia coliMutation(s): 0 
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Find proteins for U9ZUL7 (Escherichia coli 907713)
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20EB [auth y]85Escherichia coliMutation(s): 0 
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Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21FB [auth z]70Escherichia coliMutation(s): 0 
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Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 1]2903Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
16S ribosomal RNAB [auth 2]1534Escherichia coli
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S ribosomal RNAC [auth 3]120Escherichia coli
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Entity ID: 6
MoleculeChainsLengthOrganismImage
tRNA-MetF [auth 8]77Escherichia coli
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Entity ID: 7
MoleculeChainsLengthOrganismImage
mRNAG [auth 9]6Escherichia coli
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Entity ID: 59
MoleculeChainsLengthOrganismImage
transfer-messenger RNA (tmRNA)GB [auth 4]363Escherichia coli
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Entity ID: 60
MoleculeChainsLengthOrganismImage
tRNA-ValHB [auth 7]77Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BS [auth a],
CS [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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 X],
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],
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],
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],
DS [auth y],
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 7],
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 7],
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],
GS [auth 7],
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 2],
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 2],
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 2],
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 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 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 2],
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 2],
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 2],
UN [auth 2],
UO [auth 2],
UP [auth 2],
UQ [auth 2],
UR [auth 3],
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 3],
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 8],
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 8],
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 M],
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 Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
WA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: 2019-03-13 
  • 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: 2019-03-13
    Type: Initial release