7NBU

Structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history. 


Literature

Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis.

Mansour, M., Giudice, E., Xu, X., Akarsu, H., Bordes, P., Guillet, V., Bigot, D.J., Slama, N., D'urso, G., Chat, S., Redder, P., Falquet, L., Mourey, L., Gillet, R., Genevaux, P.

(2022) Nat Commun 13: 2641-2641

  • DOI: https://doi.org/10.1038/s41467-022-30373-w
  • Primary Citation of Related Structures:  
    7AWK, 7NBU

  • PubMed Abstract: 

    Toxins of toxin-antitoxin systems use diverse mechanisms to control bacterial growth. Here, we focus on the deleterious toxin of the atypical tripartite toxin-antitoxin-chaperone (TAC) system of Mycobacterium tuberculosis, whose inhibition requires the concerted action of the antitoxin and its dedicated SecB-like chaperone. We show that the TAC toxin is a bona fide ribonuclease and identify exact cleavage sites in mRNA targets on a transcriptome-wide scale in vivo. mRNA cleavage by the toxin occurs after the second nucleotide of the ribosomal A-site codon during translation, with a strong preference for CCA codons in vivo. Finally, we report the cryo-EM structure of the ribosome-bound TAC toxin in the presence of native M. tuberculosis cspA mRNA, revealing the specific mechanism by which the TAC toxin interacts with the ribosome and the tRNA in the P-site to cleave its mRNA target.

    • Organizational Affiliation: 

    Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2224Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S3206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4205Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5156Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7153Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1098Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S11117Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14100Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S1588Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1681Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1779Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1866Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1984Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2086Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2170Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Probable endoribonuclease HigB1121Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: higB1, higB, Rv1955
EC: 3.1
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2BA [auth c]271Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth d]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4DA [auth e]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5EA [auth f]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth g]176Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9GA [auth h]41Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth i]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth j]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth k]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16,50S ribosomal protein L31KA [auth l]148Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth Z]54Escherichia coli K-12Mutation(s): 0 
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Find proteins for A0A3S4NPI3 (Escherichia coli)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth m]118Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18NA [auth n]116Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth o]114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth p]117Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth q]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth r]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth s]93Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth t]102Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth u]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27VA [auth v]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28WA [auth w]77Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29XA [auth x]62Escherichia coli K-12Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30YA [auth y]58Escherichia coli K-12Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32ZA [auth z]56Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AB [auth 0]51Escherichia coli K-12Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth 1]46Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth 2]64Escherichia coli K-12Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DB [auth 3]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,539Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site fMet-tRNA(fMet)77Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
E-site tRNA2Escherichia coli K-12
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Entity ID: 24
MoleculeChains LengthOrganismImage
cspA mRNA10Mycobacterium tuberculosis H37Rv
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S ribosomal RNAZ [auth a]2,904Escherichia coli K-12
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Entity ID: 27
MoleculeChains LengthOrganismImage
5S ribosomal RNAAA [auth b]120Escherichia coli K-12
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME
Download Ideal Coordinates CCD File 
XD [auth V]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EN [auth l],
HN [auth 3]		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 a]
AC [auth A],
AD [auth A],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth a],
AI [auth a],
AJ [auth a],
AK [auth a],
AL [auth a],
AM [auth a],
AN [auth c],
BC [auth A],
BD [auth A],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth a],
BI [auth a],
BJ [auth a],
BK [auth a],
BL [auth a],
BM [auth a],
BN [auth c],
CC [auth A],
CD [auth A],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth a],
CJ [auth a],
CK [auth a],
CL [auth a],
CM [auth a],
CN [auth c],
DC [auth A],
DD [auth A],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth a],
DI [auth a],
DJ [auth a],
DK [auth a],
DL [auth a],
DM [auth a],
DN [auth d],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth a],
EF [auth a],
EG [auth a],
EH [auth a],
EI [auth a],
EJ [auth a],
EK [auth a],
EL [auth a],
EM [auth a],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FI [auth a],
FJ [auth a],
FK [auth a],
FL [auth a],
FM [auth a],
FN [auth m],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth a],
GF [auth a],
GG [auth a],
GH [auth a],
GI [auth a],
GJ [auth a],
GK [auth a],
GL [auth a],
GM [auth a],
GN [auth z],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth a],
HF [auth a],
HG [auth a],
HH [auth a],
HI [auth a],
HJ [auth a],
HK [auth a],
HL [auth a],
HM [auth a],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth a],
IF [auth a],
IG [auth a],
IH [auth a],
II [auth a],
IJ [auth a],
IK [auth a],
IL [auth a],
IM [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth a],
JF [auth a],
JG [auth a],
JH [auth a],
JI [auth a],
JJ [auth a],
JK [auth a],
JL [auth a],
JM [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth a],
KF [auth a],
KG [auth a],
KH [auth a],
KI [auth a],
KJ [auth a],
KK [auth a],
KL [auth a],
KM [auth a],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth a],
LF [auth a],
LG [auth a],
LH [auth a],
LI [auth a],
LJ [auth a],
LK [auth a],
LL [auth a],
LM [auth a],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth a],
MF [auth a],
MG [auth a],
MH [auth a],
MI [auth a],
MJ [auth a],
MK [auth a],
ML [auth a],
MM [auth a],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth a],
NF [auth a],
NG [auth a],
NH [auth a],
NI [auth a],
NJ [auth a],
NK [auth a],
NL [auth a],
NM [auth a],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth a],
OF [auth a],
OG [auth a],
OH [auth a],
OI [auth a],
OJ [auth a],
OK [auth a],
OL [auth a],
OM [auth a],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth a],
PF [auth a],
PG [auth a],
PH [auth a],
PI [auth a],
PJ [auth a],
PK [auth a],
PL [auth a],
PM [auth a],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth a],
QF [auth a],
QG [auth a],
QH [auth a],
QI [auth a],
QJ [auth a],
QK [auth a],
QL [auth a],
QM [auth a],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth a],
RF [auth a],
RG [auth a],
RH [auth a],
RI [auth a],
RJ [auth a],
RK [auth a],
RL [auth a],
RM [auth a],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth a],
SF [auth a],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
SK [auth a],
SL [auth a],
SM [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth a],
TF [auth a],
TG [auth a],
TH [auth a],
TI [auth a],
TJ [auth a],
TK [auth a],
TL [auth a],
TM [auth a],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth a],
UF [auth a],
UG [auth a],
UH [auth a],
UI [auth a],
UJ [auth a],
UK [auth a],
UL [auth a],
UM [auth a],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth a],
VF [auth a],
VG [auth a],
VH [auth a],
VI [auth a],
VJ [auth a],
VK [auth a],
VL [auth a],
VM [auth a],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth a],
WI [auth a],
WJ [auth a],
WK [auth a],
WL [auth a],
WM [auth a],
XB [auth A],
XC [auth A],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth a],
XI [auth a],
XJ [auth a],
XK [auth a],
XL [auth a],
XM [auth a],
YB [auth A],
YC [auth A],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth a],
YI [auth a],
YJ [auth a],
YK [auth a],
YL [auth a],
YM [auth b],
ZB [auth A],
ZC [auth A],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth a],
ZI [auth a],
ZJ [auth a],
ZK [auth a],
ZL [auth a],
ZM [auth b]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ		CA [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		KA [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18.2-3874
MODEL REFINEMENTCoot0.9 EL (ccp4)

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-19-CE12-0026
Swiss National Science FoundationSwitzerlandSNF CRSII3_160703

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-03-13
    Changes: Derived calculations
  • Version 2.2: 2024-04-24
    Changes: Data collection