7RH7

Mycobacterial CIII2CIV2 supercomplex, Telacebec (Q203) bound


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 2.0 of the entry. See complete history


Literature

Structure of mycobacterial CIII 2 CIV 2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203).

Yanofsky, D.J.Di Trani, J.M.Krol, S.Abdelaziz, R.Bueler, S.A.Imming, P.Brzezinski, P.Rubinstein, J.L.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.71959
  • Primary Citation of Related Structures:  
    7RH5, 7RH6, 7RH7

  • PubMed Abstract: 

    The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than 50 years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII 2 CIV 2 ). In mycobacterial electron transport chains, CIII 2 CIV 2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidoreductase activity of purified Mycobacterium smegmatis CIII 2 CIV 2 at concentrations similar to those needed to inhibit electron transfer in mycobacterial membranes and Mycobacterium tuberculosis growth in culture. We then used electron cryomicroscopy (cryoEM) to determine structures of CIII 2 CIV 2 both in the presence and absence of telacebec. The structures suggest that telacebec prevents menaquinol oxidation by blocking two different menaquinol binding modes to prevent CIII 2 CIV 2 activity.


  • Organizational Affiliation

    Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LpqE proteinA [auth W],
T [auth c]
159Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R562 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R562
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome aa3 subunit 2B [auth Q],
L [auth K]
312Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for A0R057 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R057
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1C [auth R],
M [auth L]
552Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome aa3 subunit 3D [auth S],
N [auth X]
203Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R049 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R049
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4E [auth T],
O [auth Z]
139Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for A0R056 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R056
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit CtaJF [auth U],
P [auth a]
79Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R1B6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R1B6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MSMEG_4692/MSMEI_4575G [auth V],
Q [auth b]
145Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R1B5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R1B5
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved transmembrane proteinH [auth P],
R [auth J]
100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0QVH4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]I [auth G],
S [auth D]
216Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.15.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0QQQ1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QQQ1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitJ [auth O],
U [auth I]
223Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for I7FPH1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupI7FPH1
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome b subunitK [auth E],
V [auth F]
535Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for A0R052 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex Rieske iron-sulfur subunitW [auth Y],
X [auth M]
382Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7GD61 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AC [auth F]
BC [auth F]
CC [auth F]
FA [auth R]
HA [auth S]
AC [auth F],
BC [auth F],
CC [auth F],
FA [auth R],
HA [auth S],
HB [auth L],
IA [auth S],
JB [auth X],
KA [auth T],
KB [auth X],
MA [auth P],
MB [auth Z],
NB [auth J],
XA [auth E],
YA [auth E],
ZA [auth E]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
9YF
Query on 9YF

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AB [auth E]
DC [auth F]
FC [auth Y]
GC [auth Y]
IC [auth M]
AB [auth E],
DC [auth F],
FC [auth Y],
GC [auth Y],
IC [auth M],
JC [auth M],
RA [auth O],
UB [auth I]
(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
C44 H85 O13 P
GRDWPDVMAXODDM-LZYRCPELSA-N
HEA
Query on HEA

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DA [auth R],
EA [auth R],
EB [auth L],
FB [auth L]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
MQ9
Query on MQ9

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JA [auth T]
LB [auth Z]
VA [auth E]
WA [auth E]
YB [auth F]
JA [auth T],
LB [auth Z],
VA [auth E],
WA [auth E],
YB [auth F],
ZB [auth F]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
9Y0
Query on 9Y0

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GA [auth S],
GB [auth L],
IB [auth X],
LA [auth P]
(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
C39 H76 N O8 P
DVXMEPWDARXHCX-OTMQOFQLSA-N
HEC
Query on HEC

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PA [auth O],
QA [auth O],
SB [auth I],
TB [auth I]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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SA [auth E],
TA [auth E],
VB [auth F],
WB [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9XX
Query on 9XX

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NA [auth G],
OB [auth D],
RB [auth c],
Y [auth W]
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
C38 H74 O4
LWLNRPPCJIGPLI-ZPGRZCPFSA-N
HUU (Subject of Investigation/LOI)
Query on HUU

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UA [auth E],
XB [auth F]
6-chloranyl-2-ethyl-N-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide
C29 H28 Cl F3 N4 O2
OJICYBSWSZGRFB-UHFFFAOYSA-N
PLM
Query on PLM

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OA [auth G],
PB [auth D],
QB [auth c],
Z [auth W]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FES
Query on FES

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EC [auth Y],
HC [auth M]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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AA [auth Q]
BA [auth Q]
BB [auth K]
CA [auth R]
CB [auth K]
AA [auth Q],
BA [auth Q],
BB [auth K],
CA [auth R],
CB [auth K],
DB [auth L]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaJT162186
Knut and Alice Wallenberg FoundationSweden2019.0043
Swedish Research CouncilSweden2018-04619

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 2.0: 2022-02-23
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary