5U9G

3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Mechanism of ribosome rescue by ArfA and RF2.

Demo, G.Svidritskiy, E.Madireddy, R.Diaz-Avalos, R.Grant, T.Grigorieff, N.Sousa, D.Korostelev, A.A.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.23687
  • Primary Citation of Related Structures:  
    5U9F, 5U9G

  • PubMed Abstract: 

    ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 Å resolution cryo-EM structures - determined from a single sample - of the 70S ribosome with ArfA•RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA 'senses' the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.


  • Organizational Affiliation

    RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Alternative ribosome-rescue factor AD [auth Y]72Escherichia coli K-12Mutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1F [auth 03]234Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2G [auth 04]273Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3H [auth 05]209Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4I [auth 06]201Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5J [auth 07]179Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6K [auth 08]177Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9L [auth 09]149Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10M [auth 10]165Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11N [auth 11]142Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth 12]142Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P [auth 13]123Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15Q [auth 14]144Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth 15]136Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth 16]127Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18T [auth 17]117Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19U [auth 18]115Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20V [auth 19]118Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21W [auth 20]103Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22X [auth 21]110Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth 22]100Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth 23]104Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AA [auth 24]94Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BA [auth 25]85Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth 26]78Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth 27]63Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth 28]59Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31FA [auth 29]70Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32GA [auth 30]57Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33HA [auth 31]55Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34IA [auth 32]46Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35JA [auth 33]65Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36KA [auth 34]38Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor RF2NA [auth Z]365Escherichia coli K-12Mutation(s): 0 
Gene Names: prfBsupKb2891JW5847
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2OA [auth B]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3PA [auth C]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4QA [auth D]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5RA [auth E]167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6SA [auth F]131Escherichia coliMutation(s): 0 
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30S ribosomal protein S7TA [auth G]156Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8UA [auth H]130Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9VA [auth I]130Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10WA [auth J]103Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11XA [auth K]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12YA [auth L]124Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13ZA [auth M]118Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14AB [auth N]101Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15BB [auth O]89Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16CB [auth P]82Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17DB [auth Q]84Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18EB [auth R]75Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19FB [auth S]92Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20GB [auth T]87Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21HB [auth U]71Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,539Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S ribosomal RNAB [auth 01]2,903Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 02]119Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
fMet-tRNA (P- and E-site)E [auth X],
MA [auth W]
77Escherichia coli
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Entity ID: 38
MoleculeChains LengthOrganismImage
truncated mRNALA [auth V]14Escherichia 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 
PO [auth 34]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth 01]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth 01],
AH [auth 01],
AI [auth 01],
AJ [auth 01],
AK [auth 01],
AL [auth 01],
AM [auth 01],
AN [auth 01],
AO [auth 01],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth 01],
BG [auth 01],
BH [auth 01],
BI [auth 01],
BJ [auth 01],
BK [auth 01],
BL [auth 01],
BM [auth 01],
BN [auth 01],
BO [auth 01],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth 01],
CG [auth 01],
CH [auth 01],
CI [auth 01],
CJ [auth 01],
CK [auth 01],
CL [auth 01],
CM [auth 01],
CN [auth 01],
CO [auth 01],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth 01],
DG [auth 01],
DH [auth 01],
DI [auth 01],
DJ [auth 01],
DK [auth 01],
DL [auth 01],
DM [auth 01],
DN [auth 01],
DO [auth 01],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth 01],
EG [auth 01],
EH [auth 01],
EI [auth 01],
EJ [auth 01],
EK [auth 01],
EL [auth 01],
EM [auth 01],
EN [auth 01],
EO [auth 01],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth 01],
FG [auth 01],
FH [auth 01],
FI [auth 01],
FJ [auth 01],
FK [auth 01],
FL [auth 01],
FM [auth 01],
FN [auth 01],
FO [auth 01],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth 01],
GG [auth 01],
GH [auth 01],
GI [auth 01],
GJ [auth 01],
GK [auth 01],
GL [auth 01],
GM [auth 01],
GN [auth 01],
GO [auth 02],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth 01],
HG [auth 01],
HH [auth 01],
HI [auth 01],
HJ [auth 01],
HK [auth 01],
HL [auth 01],
HM [auth 01],
HN [auth 01],
HO [auth 02],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth 01],
IG [auth 01],
IH [auth 01],
II [auth 01],
IJ [auth 01],
IK [auth 01],
IL [auth 01],
IM [auth 01],
IN [auth 01],
IO [auth 02],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth 01],
JG [auth 01],
JH [auth 01],
JI [auth 01],
JJ [auth 01],
JK [auth 01],
JL [auth 01],
JM [auth 01],
JN [auth 01],
JO [auth 02],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth 01],
KG [auth 01],
KH [auth 01],
KI [auth 01],
KJ [auth 01],
KK [auth 01],
KL [auth 01],
KM [auth 01],
KN [auth 01],
KO [auth X],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth 01],
LG [auth 01],
LH [auth 01],
LI [auth 01],
LJ [auth 01],
LK [auth 01],
LL [auth 01],
LM [auth 01],
LN [auth 01],
LO [auth X],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth 01],
MG [auth 01],
MH [auth 01],
MI [auth 01],
MJ [auth 01],
MK [auth 01],
ML [auth 01],
MM [auth 01],
MN [auth 01],
MO [auth 14],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth 01],
NG [auth 01],
NH [auth 01],
NI [auth 01],
NJ [auth 01],
NK [auth 01],
NL [auth 01],
NM [auth 01],
NN [auth 01],
NO [auth 25],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth 01],
OG [auth 01],
OH [auth 01],
OI [auth 01],
OJ [auth 01],
OK [auth 01],
OL [auth 01],
OM [auth 01],
ON [auth 01],
OO [auth 30],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth 01],
PG [auth 01],
PH [auth 01],
PI [auth 01],
PJ [auth 01],
PK [auth 01],
PL [auth 01],
PM [auth 01],
PN [auth 01],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth 01],
QG [auth 01],
QH [auth 01],
QI [auth 01],
QJ [auth 01],
QK [auth 01],
QL [auth 01],
QM [auth 01],
QN [auth 01],
QO [auth W],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth 01],
RG [auth 01],
RH [auth 01],
RI [auth 01],
RJ [auth 01],
RK [auth 01],
RL [auth 01],
RM [auth 01],
RN [auth 01],
RO [auth W],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth 01],
SG [auth 01],
SH [auth 01],
SI [auth 01],
SJ [auth 01],
SK [auth 01],
SL [auth 01],
SM [auth 01],
SN [auth 01],
SO [auth H],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth 01],
TG [auth 01],
TH [auth 01],
TI [auth 01],
TJ [auth 01],
TK [auth 01],
TL [auth 01],
TM [auth 01],
TN [auth 01],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth 01],
UG [auth 01],
UH [auth 01],
UI [auth 01],
UJ [auth 01],
UK [auth 01],
UL [auth 01],
UM [auth 01],
UN [auth 01],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth 01],
VG [auth 01],
VH [auth 01],
VI [auth 01],
VJ [auth 01],
VK [auth 01],
VL [auth 01],
VM [auth 01],
VN [auth 01],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth 01],
WG [auth 01],
WH [auth 01],
WI [auth 01],
WJ [auth 01],
WK [auth 01],
WL [auth 01],
WM [auth 01],
WN [auth 01],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth 01],
XG [auth 01],
XH [auth 01],
XI [auth 01],
XJ [auth 01],
XK [auth 01],
XL [auth 01],
XM [auth 01],
XN [auth 01],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth 01],
YG [auth 01],
YH [auth 01],
YI [auth 01],
YJ [auth 01],
YK [auth 01],
YL [auth 01],
YM [auth 01],
YN [auth 01],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth 01],
ZG [auth 01],
ZH [auth 01],
ZI [auth 01],
ZJ [auth 01],
ZK [auth 01],
ZL [auth 01],
ZM [auth 01],
ZN [auth 01]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRSRef
MODEL REFINEMENTPHENIX
RECONSTRUCTIONFREALIGN9.11

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106105

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Data collection, Experimental preparation
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Derived calculations