5IQR

Structure of RelA bound to the 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Ribosome-dependent activation of stringent control.

Brown, A.Fernandez, I.S.Gordiyenko, Y.Ramakrishnan, V.

(2016) Nature 534: 277-280

  • DOI: 10.1038/nature17675
  • Primary Citation of Related Structures:  
    5IQR

  • PubMed Abstract: 
  • In order to survive, bacteria continually sense, and respond to, environmental fluctuations. Stringent control represents a key bacterial stress response to nutrient starvation that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns ...

    In order to survive, bacteria continually sense, and respond to, environmental fluctuations. Stringent control represents a key bacterial stress response to nutrient starvation that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns. In general, transcription of genes for growth and proliferation is downregulated, while those important for survival and virulence are upregulated. Amino acid starvation is sensed by depletion of the aminoacylated tRNA pools, and this results in accumulation of ribosomes stalled with non-aminoacylated (uncharged) tRNA in the ribosomal A site. RelA is recruited to stalled ribosomes and activated to synthesize a hyperphosphorylated guanosine analogue, (p)ppGpp, which acts as a pleiotropic secondary messenger. However, structural information about how RelA recognizes stalled ribosomes and discriminates against aminoacylated tRNAs is missing. Here we present the cryo-electron microscopy structure of RelA bound to the bacterial ribosome stalled with uncharged tRNA. The structure reveals that RelA utilizes a distinct binding site compared to the translational factors, with a multi-domain architecture that wraps around a highly distorted A-site tRNA. The TGS (ThrRS, GTPase and SpoT) domain of RelA binds the CCA tail to orient the free 3' hydroxyl group of the terminal adenosine towards a β-strand, such that an aminoacylated tRNA at this position would be sterically precluded. The structure supports a model in which association of RelA with the ribosome suppresses auto-inhibition to activate synthesis of (p)ppGpp and initiate the stringent response. Since stringent control is responsible for the survival of pathogenic bacteria under stress conditions, and contributes to chronic infections and antibiotic tolerance, RelA represents a good target for the development of novel antibacterial therapeutics.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.



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50S ribosomal protein L2A [auth B]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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50S ribosomal protein L3B [auth C]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L4C [auth D]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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50S ribosomal protein L5D [auth E]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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50S ribosomal protein L6E [auth F]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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50S ribosomal protein L9F [auth G]149Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L10G [auth H]165Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L11H [auth I]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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50S ribosomal protein L13I [auth J]142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14J [auth K]123Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L15K [auth L]144Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L16L [auth M]136Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L17M [auth N]127Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18N [auth O]117Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L19O [auth P]115Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L20P [auth Q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21Q [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22R [auth S]110Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L23S [auth T]100Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L24T [auth U]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25U [auth V]94Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L27V [auth W]85Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L28W [auth X]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29X [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L30Y [auth Z]59Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L31Z [auth a]70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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50S ribosomal protein L32AA [auth b]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33BA [auth c]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34CA [auth d]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35DA [auth e]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36EA [auth f]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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30S ribosomal protein S2FA [auth g]241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3GA [auth h]233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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30S ribosomal protein S4HA [auth i]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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30S ribosomal protein S5IA [auth j]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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30S ribosomal protein S6JA [auth k]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S7KA [auth l]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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30S ribosomal protein S8LA [auth m]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9MA [auth n]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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30S ribosomal protein S10NA [auth o]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11OA [auth p]129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12PA [auth q]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13QA [auth r]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14RA [auth s]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth t]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth u]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth v]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth w]75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19WA [auth x]92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth y]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21YA [auth z]71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
GTP pyrophosphokinaseGB [auth 8]744Escherichia coli K-12Mutation(s): 0 
Gene Names: relAb2784JW2755
EC: 2.7.6.5
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Entity ID: 52
MoleculeChainsLengthOrganismImage
LSU rRNAZA [auth 1]2904Escherichia coli K-12
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Entity ID: 53
MoleculeChainsLengthOrganismImage
SSU rRNAAB [auth 2]1533Escherichia coli K-12
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Entity ID: 54
MoleculeChainsLengthOrganismImage
5S rRNABB [auth 3]118Escherichia coli K-12
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Entity ID: 55
MoleculeChainsLengthOrganismImage
E-site tRNA(Phe)CB [auth 4]76Escherichia coli K-12
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Entity ID: 56
MoleculeChainsLengthOrganismImage
P-site fMet-tRNA(fMet)DB [auth 5]78Escherichia coli K-12
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Entity ID: 57
MoleculeChainsLengthOrganismImage
A/T tRNA(Phe)EB [auth 6]76Escherichia coli K-12
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Entity ID: 58
MoleculeChainsLengthOrganismImage
mRNAFB [auth 7]10synthetic construct
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
PM [auth 2]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
MET
Query on MET

Download Ideal Coordinates CCD File 
WM [auth 5]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NB [auth a],
OB [auth f],
YM [auth 8]
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 2],
AM [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 2],
BM [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 2],
CM [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 2],
DL [auth 2],
DM [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 2],
EL [auth 2],
EM [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 2],
FL [auth 2],
FM [auth 2],
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 2],
GL [auth 2],
GM [auth 2],
HB [auth B],
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 2],
HL [auth 2],
HM [auth 2],
IB [auth C],
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 2],
IL [auth 2],
IM [auth 2],
JB [auth L],
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 2],
JL [auth 2],
JM [auth 2],
KB [auth L],
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 2],
KL [auth 2],
KM [auth 2],
LB [auth N],
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 2],
LL [auth 2],
LM [auth 2],
MB [auth U],
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 2],
ML [auth 2],
MM [auth 2],
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 2],
NL [auth 2],
NM [auth 2],
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 2],
OL [auth 2],
OM [auth 2],
PB [auth r],
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 2],
PL [auth 2],
QB [auth s],
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 2],
QL [auth 2],
QM [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 2],
RL [auth 2],
RM [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 2],
SL [auth 2],
SM [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 2],
TL [auth 2],
TM [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 2],
UL [auth 2],
UM [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 2],
VL [auth 2],
VM [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 2],
WL [auth 2],
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 2],
XL [auth 2],
XM [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 2],
YL [auth 2],
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 2],
ZL [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
D2T
Query on D2T
PA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 2.0: 2017-08-02
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2018-03-07
    Changes: Source and taxonomy
  • Version 3.0: 2018-10-17
    Changes: Data collection, Polymer sequence, Refinement description