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 7SFR | pdb_00007sfr

Unmethylated Mtb Ribosome 50S with SEQ-9


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history. 

Literature

Discovery of natural-product-derived sequanamycins as potent oral anti-tuberculosis agents.

Zhang, J., Lair, C., Roubert, C., Amaning, K., Barrio, M.B., Benedetti, Y., Cui, Z., Xing, Z., Li, X., Franzblau, S.G., Baurin, N., Bordon-Pallier, F., Cantalloube, C., Sans, S., Silve, S., Blanc, I., Fraisse, L., Rak, A., Jenner, L.B., Yusupova, G., Yusupov, M., Zhang, J., Kaneko, T., Yang, T.J., Fotouhi, N., Nuermberger, E., Tyagi, S., Betoudji, F., Upton, A., Sacchettini, J.C., Lagrange, S.

(2023) Cell 186: 1013

  • DOI: https://doi.org/10.1016/j.cell.2023.01.043
  • Primary Citation Related Structures: 
    7AZO, 7AZS, 7KGB, 7SFR

  • PubMed Abstract: 

    The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding in vitro and in vivo activity against Mycobacterium tuberculosis (Mtb). Sequanamycins are bacterial ribosome inhibitors that interact with the ribosome in a similar manner to classic macrolides like erythromycin and clarithromycin, but with binding characteristics that allow them to overcome the inherent macrolide resistance of Mtb. Structures of the ribosome with bound inhibitors were used to optimize sequanamycin to produce the advanced lead compound SEQ-9. SEQ-9 was efficacious in mouse models of acute and chronic TB as a single agent, and it demonstrated bactericidal activity in a murine TB infection model in combination with other TB drugs. These results support further investigation of this series as TB clinical candidates, with the potential for use in new regimens against drug-susceptible and drug-resistant TB.


  • Organizational Affiliation: 
    • Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France.

Macromolecule Content 

  • Total Structure Weight: 2,243.57 kDa 
  • Atom Count: 143,665 
  • Modeled Residue Count: 10,013 
  • Deposited Residue Count: 10,944 
  • Unique protein chains: 48
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33B [auth 1]55Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]47Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]64Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]37Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31F [auth 6]80Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth C]279Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3J [auth D]213Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4K [auth E]207Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5L [auth F]178Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6M [auth G]177Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L9N [auth H]152Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth J]195Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P [auth K]122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15Q [auth L]146Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth M]138Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth N]180Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18T [auth O]122Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19U [auth P]113Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20V [auth Q]129Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21W [auth R]104Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22X [auth S]197Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth T]100Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth U]105Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045IXU4 (Mycobacterium tuberculosis)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AA [auth V]215Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BA [auth W]86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth X]64Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth Y]77Mycobacterium tuberculosisMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth Z]65Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for A0A045H4J2 (Mycobacterium tuberculosis)
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3GA [auth c]274Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4HA [auth d]201Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S5IA [auth e]220Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6JA [auth f]96Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7KA [auth g]156Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8LA [auth h]132Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9MA [auth i]151Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S10NA [auth j]101Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11OA [auth k]139Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12PA [auth l]124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13QA [auth m]124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZRA [auth n]61Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth o]89Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth p]162Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth q]135Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth r]84Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19WA [auth s]93Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth t]86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
peptideYA [auth v]22Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 7
MoleculeChains LengthOrganismImage
23S rRNAG [auth A]3,138Mycobacterium tuberculosis
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S rRNAH [auth B]115Mycobacterium tuberculosis
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Entity ID: 32
MoleculeChains LengthOrganismImage
16S rRNAFA [auth a]1,537Mycobacterium tuberculosis
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Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WDP
(Subject of Investigation/LOI)

Query on WDP



Download:Ideal Coordinates CCD File
CB [auth A]Sequanamycin 9
C61 H102 N4 O20 S
IXJRUHKGLMWLLP-XMRFQGNKSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AB [auth 4]
BB [auth 6]
IS [auth n]
JS [auth r]
LN [auth X]
AB [auth 4],
BB [auth 6],
IS [auth n],
JS [auth r],
LN [auth X],
ZA [auth 1]
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 B],
AO [auth a],
AP [auth a],
AQ [auth a],
AR [auth a],
AS [auth a],
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 B],
BO [auth a],
BP [auth a],
BQ [auth a],
BR [auth a],
BS [auth a],
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 B],
CO [auth a],
CP [auth a],
CQ [auth a],
CR [auth a],
CS [auth a],
DB [auth A],
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 B],
DO [auth a],
DP [auth a],
DQ [auth a],
DR [auth a],
DS [auth a],
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],
EN [auth B],
EO [auth a],
EP [auth a],
EQ [auth a],
ER [auth a],
ES [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 C],
FO [auth a],
FP [auth a],
FQ [auth a],
FR [auth a],
FS [auth a],
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 C],
GO [auth a],
GP [auth a],
GQ [auth a],
GR [auth a],
GS [auth a],
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],
HN [auth C],
HO [auth a],
HP [auth a],
HQ [auth a],
HR [auth a],
HS [auth e],
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],
IN [auth D],
IO [auth a],
IP [auth a],
IQ [auth a],
IR [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],
JN [auth L],
JO [auth a],
JP [auth a],
JQ [auth a],
JR [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],
KN [auth M],
KO [auth a],
KP [auth a],
KQ [auth a],
KR [auth a],
KS [auth t],
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],
LO [auth a],
LP [auth a],
LQ [auth a],
LR [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],
MN [auth a],
MO [auth a],
MP [auth a],
MQ [auth a],
MR [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],
NN [auth a],
NO [auth a],
NP [auth a],
NQ [auth a],
NR [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],
ON [auth a],
OO [auth a],
OP [auth a],
OQ [auth a],
OR [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],
PN [auth a],
PO [auth a],
PP [auth a],
PQ [auth a],
PR [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],
QN [auth a],
QO [auth a],
QP [auth a],
QQ [auth a],
QR [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],
RN [auth a],
RO [auth a],
RP [auth a],
RQ [auth a],
RR [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],
SN [auth a],
SO [auth a],
SP [auth a],
SQ [auth a],
SR [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],
TN [auth a],
TO [auth a],
TP [auth a],
TQ [auth a],
TR [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],
UN [auth a],
UO [auth a],
UP [auth a],
UQ [auth a],
UR [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],
VN [auth a],
VO [auth a],
VP [auth a],
VQ [auth a],
VR [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],
WN [auth a],
WO [auth a],
WP [auth a],
WQ [auth a],
WR [auth a],
XB [auth A],
XC [auth A],
XD [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],
XN [auth a],
XO [auth a],
XP [auth a],
XQ [auth a],
XR [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],
YN [auth a],
YO [auth a],
YP [auth a],
YQ [auth a],
YR [auth a],
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],
ZN [auth a],
ZO [auth a],
ZP [auth a],
ZQ [auth a],
ZR [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1

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 StatesP01AI095208
Welch FoundationUnited StatesA1863

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references, Refinement description
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2024-06-05
    Changes: Data collection, Refinement description
  • Version 2.0: 2026-07-01
    Changes: Atomic model, Data collection, Database references, Structure summary