7E1V

Cryo-EM structure of apo hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Mycobacterium tuberculosis cytochrome bcc in complex with Q203 and TB47, two anti-TB drug candidates.

Zhou, S.Wang, W.Zhou, X.Zhang, Y.Lai, Y.Tang, Y.Xu, J.Li, D.Lin, J.Yang, X.Ran, T.Chen, H.Guddat, L.W.Wang, Q.Gao, Y.Rao, Z.Gong, H.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.69418
  • Primary Citation of Related Structures:  
    7E1V, 7E1W, 7E1X

  • PubMed Abstract: 

    Pathogenic mycobacteria pose a sustained threat to global human health. Recently, cytochrome bcc complexes have gained interest as targets for antibiotic drug development. However, there is currently no structural information for the cytochrome bcc complex from these pathogenic mycobacteria. Here, we report the structures of Mycobacterium tuberculosis cytochrome bcc alone (2.68 Å resolution) and in complex with clinical drug candidates Q203 (2.67 Å resolution) and TB47 (2.93 Å resolution) determined by single-particle cryo-electron microscopy. M. tuberculosis cytochrome bcc forms a dimeric assembly with endogenous menaquinone/menaquinol bound at the quinone/quinol-binding pockets. We observe Q203 and TB47 bound at the quinol-binding site and stabilized by hydrogen bonds with the side chains of QcrB Thr 313 and QcrB Glu 314 , residues that are conserved across pathogenic mycobacteria. These high-resolution images provide a basis for the design of new mycobacterial cytochrome bcc inhibitors that could be developed into broad-spectrum drugs to treat mycobacterial infections.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2A [auth E],
H [auth Q]
341Mycolicibacterium smegmatis MC2 51Mutation(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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1B [auth F],
I [auth R]
575Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C [auth G],
J [auth S]
203Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
EC: 7.1.1.9
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4D [auth H],
K [auth T]
139Mycolicibacterium smegmatis MC2 51Mutation(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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit CtaJE [auth I],
L [auth U]
79Mycolicibacterium smegmatis MC2 51Mutation(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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MSMEG_4692/MSMEI_4575F [auth J],
M [auth V]
157Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
UniProt
Find proteins for A0R1B5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Prokaryotic respiratory supercomplex associate factor 1 PRSAF1G [auth D],
N [auth P]
100Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0QVH4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome b subunitO [auth N],
R [auth B]
549Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: qcrBRv2196MTCY190.07
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P9WP37 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex Rieske iron-sulfur subunitP [auth M],
S [auth A]
429Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: qcrARv2195MTCY190.06
Membrane Entity: Yes 
UniProt
Find proteins for P9WH23 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitQ [auth O],
T [auth C]
280Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: qcrCRv2194MTCY190.05
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P9WP35 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AC [auth C]
CB [auth M]
EA [auth D]
IA [auth R]
JA [auth R]
AC [auth C],
CB [auth M],
EA [auth D],
IA [auth R],
JA [auth R],
MB [auth B],
NB [auth B],
OB [auth B],
PA [auth P],
PB [auth B],
SA [auth N],
UA [auth N],
VA [auth N],
W [auth F],
WA [auth N],
X [auth F],
XB [auth C]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
9YF
Query on 9YF

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DB [auth M],
EB [auth M],
TB [auth A],
UB [auth A]
(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 (Subject of Investigation/LOI)
Query on HEA

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BA [auth F],
CA [auth F],
MA [auth R],
NA [auth R]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
MQ9 (Subject of Investigation/LOI)
Query on MQ9

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AB [auth N]
FB [auth O]
GB [auth O]
QB [auth B]
RB [auth B]
AB [auth N],
FB [auth O],
GB [auth O],
QB [auth B],
RB [auth B],
XA [auth N],
YA [auth N],
YB [auth C],
ZA [auth N],
ZB [auth C]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
9Y0 (Subject of Investigation/LOI)
Query on 9Y0

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DA [auth G],
OA [auth S]
(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
C39 H76 N O8 P
DVXMEPWDARXHCX-OTMQOFQLSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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HB [auth O],
IB [auth O],
VB [auth C],
WB [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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KB [auth B],
LB [auth B],
QA [auth N],
RA [auth N]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PLM (Subject of Investigation/LOI)
Query on PLM

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JB [auth B],
KA [auth R],
TA [auth N],
Y [auth F]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FES
Query on FES

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BB [auth M],
SB [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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AA [auth F]
FA [auth Q]
GA [auth Q]
HA [auth Q]
LA [auth R]
AA [auth F],
FA [auth Q],
GA [auth Q],
HA [auth Q],
LA [auth R],
U [auth E],
V [auth E],
Z [auth F]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37030201
Chinese Academy of SciencesChinaXDB37020203
Chinese Academy of SciencesChina2017YFC0840300
National Natural Science Foundation of China (NSFC)China81520108019
National Natural Science Foundation of China (NSFC)China813300237

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2022-07-27
    Changes: Database references